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Final Report

PESCADERO MARSH
Restoration Assessment and Recommendations for
Ecosystem Management

Prepared for March 2008


Califomia Department of Parks and Recreation
Final Report

PESCADERO MARSH
Restoration Assessment and Recommendations for
Ecosystem Management

Prepared for March 2008


Califomia Department of Parks and Recreation
95 Kelly Ave.
Half Moon Bay, CA 94019

225 Bush Street


Su~e 1700
San Francisco. CA 94104
415.896.5900
www.esassoc.com

Los Angeles

Oakland

Olympia

Petaluma

Portland

Sacramento

San Diego

Seattle

Tampa

Woodland Hills

202117

r-- ESA
~
TABLE OF CONTENTS
Pescadero Marsh Restoration Assessment and
Recommendations for Ecosystem Management

I. Introduction 1
A. Project Purpose, Goals, and Objectives 4
B. Methods 5
C. Changes from the Original Scope of Work 8
D. Adaptive Management 10

II. Review of the 1990 Enhancement Plan 13

III. Results: Historical Changes, Current Conditions, and Recommendations 17


A. North Pond and North Marsh 17
B. Butano Marshes 43
C. Delta Marshes 54
D. Butano Creek 61
E. Pescadero Creek 68
F. Lagoon 75

IV. Report Authors and Contributors 87

References 89

Appendices
A. Pescadero Marsh Vegetation Transect Analysis Technical Report A-1
B. Re-Survey of the 1987 Pescadero Marsh Cross-sections on Pescadero Creek B-1
C. Butano Creek Cross-sections Survey Report C-1
D. Survey of the Pescadero Creek Outlet Channel D-1
E. Water Quality Data E-1

PescaderoMarshRestorationAssessmentand ESA1202117
Recommendations
for EcosystemManagement Mardl 2008
Table of Contents

List of Figures
Figure 1: Location Map 2
Figure 2: Land Cover and Place Nam es Map 3
Figure 3: Vegetation Transects Map 6
Figure 4: Water Quality Stations Map 7
Figure 5: Pescadero Lagoon, 1915 and 2002 11
Figure 6: U.S. Coast Survey Map of Pescadero Marsh, 1854 18
Figure 7: Aerial Photograph: 1928 19
Figure 8: Aerial Photograph: 1941 20
Figure 9: Aerial Photograph: May 27, 1956 21
Figure 10: Aerial Photograph: March 26, 1986 22
Figure 11: Aerial Photograph: 2002 23
Figure 12: Elevation of the Top of the Low Levee 29
Figure 13: Marsh Water Level 31
Figure 14: Station C1 Water Quality 32
Figure 15: Station C2 Vertical Profile 33
Figure 16: Station C3 Water Quality 34
Figure 17: Station E1 Water Quality 35
Figure 18: Station F2 Vertical Profile 36
Figure 19: Water Temperature at Station C1 37
Figure 20: Pescadero Marsh Air Temperature 38
Figure 21 Station 03 Water Quality 48
Figure 22: Station WL Water Quality 49
Figure 23: Station WL Water Temperature 50
Figure 24: Station G1 Water Temperature 57
Figure 25: Station XS-11 Water Temperature 64
Figure 26: Station XS-7 Water Temperature 65
Figure 27: Station P1 Water Quality 72
Figure 28: Station A Water Quality 80
Figure 29: Tidal Velocity 81

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Reconrnendations for Ecosystem Managerrent March 2008
CHAPTER I
Introduction

Pescadero Marsh is an approximately 340-acre coastal wetland formed at the confluence of


Pescadero Creek and Butano Creek in San Mateo County, California. It is located about 12 miles
south of the City of Half Moon Bay, at the intersection of State Highway 1 and Pescadero Road
(Figure 1). Pescadero Marsh (the Marsh) encompasses Pescadero Lagoon, the lower courses of
the two creeks, and some adjacent upland areas (Figure 2). The Marsh is within Pescadero State
Beach; a 225 acre section of the Marsh is classified as Pescadero Marsh Natural Preserve.
Pescadero Marsh offers a diversity of habitats, including salt marsh, fresh water marsh, sand
dune, riparian forest, and coastal scrub. The Marsh changes seasonally from an open, tidal estuary
to a closed lagoon, the result of a sandbar that forms across the mouth of Pescadero Creek during
the spring, summer, or fall, and that persists usually until late fall or early winter. After formation
of the sandbar, the water level in the lagoon and throughout the Marsh rises, inundating the
lowland areas of the Marsh.

Pescadero Marsh provides habitat for a wide variety offish, birds, amphibians, reptiles,
invertebrates, and plants. Over the course of the twentieth century, much of this habitat was
degraded or eliminated, due to diking and draining of most of the marsh areas, and their
conversion to agricultural uses. In addition, the construction of State Highway 1 across the
western edge of the Marsh; the construction of Pescadero Road and the bridge over Butano
Creek; and alterations in the watersheds of Pescadero and Butano Creeks that led to a huge
increase in the sediment load carried by the two streams (ESA, 2004) and a decrease in dry
season flows - all wrought major changes on the Marsh.

The California Department of Parks and Recreation (DPR) began purchasing land for Pescadero
State Beach in 1958, and completed acquisition of the currently-held parcels in 1979.1 Since DPR
took ownership of the Marsh, it has engaged in a series of studies to better understand Marsh
dynamics and past conditions, and has undertaken a series of actions to restore the natural
hydrologic functions and biological productivity of the Marsh. This report represents the latest
effort in this series.

1 DPR acquired a conservation easement on an additional parcel in 1993.

Pescadero Marsh Restoration Assessment and ESA/202117


Recorrmendations for Ecosystem Managerrent March 2008
Stanislaus

Pescadero Marsh

0
t 12
L.. I
Miles

--------------------------- Pescadero Marsh Natural Preserve Res/oration Assessment/202//7 -


Figure 1
Location
~
"'I:{ Legend

'4 o Preserve Boundary


II
ighway
C) ~
~M,yorRoad
J'V'Road

NStref!lfls and Waterways

NLevees
II _ Riparim Tree Canopy

"
Open Waer
Marm
~ Upland

"
Eucalyptus
II Sand Dune
Agriculture and Residential
._,.
"'I:{ Beach
Q." ..
Q,
..... Fallow
t:1 G;j Paved or Graded
C;

A ~--
500

100
0

p-a.-0
500 1000 Feet

100 200 300 Meters


i

--------------------------------------PescatkroMarshNatural Preserve
RstorationAssessment/202117.
SOURCE: Environmental Science Associates.
California Department of Parks and Recreation.
Figure 2
U.S. Geological Survey Land Cover and Place Names
I. Introduction

A. Project Purpose, Goals, and Objectives


This report presents the results of studies conducted by Environmental Science Associates (ESA)
and Dennis Jackson, Hydrologist, in Pescadero Marsh in 2001, 2002, and 2003. The purpose of
the project was to ascertain current conditions in the Marsh, focusing on hydrology,
geomorphology, and biology. In particular, the purpose was to repeat several surveys conducted
by other parties for DPR in the 1980s, in order to ascertain changes that have occurred in the
Marsh since several restoration projects were undertaken in the 1990s, with a secondary focus on
the patterns of change in the Marsh over time. The restoration projects grew out of
recommendations made in a plan (the Enhancement Plan) prepared by Philip Williams and
Associates for DPR in 1990 (Williams, 1990), which was itself based largely on the studies
undertaken during the 1980s.

This report makes recommendations for future management of the Marsh consistent with DPR's
overall management goals. The recommendations are preliminary, and will require significant
further study and analysis prior to proceeding with any action. DPR's current management goals
for Pescadero Marsh include the following:

1. Pescadero Marsh should be managed as a natural system that functions as it did prior to
human disturbance, to the extent possible and discernible.

2. The Marsh should be managed for the benefit of the special status species that occur there,
including steelhead trout (Oncorhynchus mykiss), California red-legged frog (Rana aurora
draytonii), San Francisco garter snake (Thamnnophis sirtalis tetrataenia), and tidewater goby
(Eucyclogobius newberryi).

3. The Marsh should be managed so that it contains a diversity of wetland and upland habitat
types, assuming that this would mimic pre-disturbance conditions. This includes freshwater,
brackish, and saltwater marshes; riparian forests; sand dunes; and coastal scrub.

4. To the extent possible, active management should be kept to a minimum: systems and
enhancements should be passive and self-sustaining.

5. The Marsh should be allowed to evolve naturally: change should be accepted as an inevitable
and desirable condition.

6. Recreational opportunities, consistent with the other goals, should be maintained and
enhanced.

7. An adaptive management program will be used to ascertain the effects of management


decisions and to guide future management toward achievement of the goals.

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Recorrmendations for Ecosystem Managerrent March 2008
I. Introduction

B. Methods
Methods included a review of prior studies on the Marsh prepared for and by DPR (Curry et al,
1985; Jennings and Hayes, 1990; Smith, 1987; Smith and Reis, 1997; Swanson, 1987; Williams,
1990), and several phases offield work. Field work methods included the following:

Re-surveys- of stream channel and lagoon cross sections, originally surveyed in 1987, to
ascertain changes in channel morphology and streambed base elevation. Cross section
surveys were begun in fall, 2001 under a separate contract with DPR, and completed in the
fall of2002. 16 of the 33 cross sections first surveyed in 1987 were re-surveyed. Survey
methods, cross section locations, and results are detailed in appendices Band C. Results are
discussed below.

Re-survey often vegetation transects, originally established and surveyed in 1985 as to


species presence and relative abundance (Figure 3). DPR staff conducted additional surveys
of the transects in 1986, 1987, and 1990, and ESA re-surveyed them in 2003 and compared
the results to the previous surveys. Detailed methods and results are included in Appendix
A.

Water level of the Marsh was monitored continuously' from May 22, 2002 through April
15,2003 near the footbridge over the levee break on Butano Creek at water quality station
WL (Figure 4). Monitoring was accomplished with a Global Water model WL-15 data
logger, set within a 2 inch diameter perforated plastic pipe. The sensor was set at the
channel bottom, and registered water depth above it. Water level readings were recorded
every 15 minutes, and the data were downloaded periodically, and corrected to read water
surface. A crest gauge was used to ascertain the water level at high tide near the low spot in
the low levee on the west side of North Marsh, at water quality station C3 (Figure 4) on
(August 8, 2002), during one ofthe predicted highest tides of the year. A perforated plastic
pipe was slipped over a staff gauge and cork crumbles were placed within the plastic pipe.
The cork crumbles stuck to the staff gauge at the highest level that the water achieved, and
were read the next morning. Results are discussed below.

The mouth of Pescadero Creek was surveyed on two occasions in the winter and spring of
2003 to ascertain hydraulic conditions and channel morphology during ebb tides. The
survey methods and results are presented in Appendix D.

Water quality was monitored at several stations originally established by Smith, and
discussed in Smith and Reis (1997). Not all of these stations were monitored, and other
stations were added. Our monitoring occurred in summer and fall, 2002. Department of
Parks and Recreation personnel conducted additional monitoring in 2003 and 2004.
Monitoring was accomplished with a Yellowsprings Equipment Inc. model YSI-85 multi-
parameter meter, which takes and records simultaneous readings of temperature, dissolved

2 All elevations stated in this report use the 1929 National Geodetic Vertical Datum (NGVD-29), in order to conform
with the standard used in earlier studies, and thus avoid confusion. To convert to the current datum, NAVD-88, at
Pescadero Marsh, add 2.67 feet.
3 A rapid rise in marsh water level, associated with the first runoff event of the season and high waves which
overtopped the sandbar, inundated the data logger on November 8, 2002. The instrument continued to operate, but
did not record water level accurately for several days, and then ceased to function. The unit was replaced on
November 21, and the record is complete from that point on. The inaccurate readings and the data gap can be seen
in Figure 13.

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Recorrmendations for Ecosystem Management March 2008
Legend
Nvegetanon Transects
Theme1shp
D Preserve Boundary
Roads
~ighWay
~MajorRoad
i";'Road

NStreams and Waterways

NLevees

_ Riparian Tree Canopy


_OpenWater
Marsh
Upland
Eucalyptus
Sand Dune
::>::::: Agriculture and Residential
Beach
::~::~~,::~.
Fall ow
EJ Paved or Graded

0
A
500 1000 1500 Feet
i i

SOURCE: ESA
Legend
Water Quality Stations
Temperature logger
(!) TVIAJtemperature loggers
I!I Water temperature and level
4. Waterandairtemperature
o Spot monitoring

o Preserve Boundary

~ighway
~MajOrROad
~Road

NStreams and Waterways

NLevees

_ Riparian Tree Canopy


_OpenWater
Marsh
Upland
Eucalyptus
Sand Dune
Agriculture and Residential
Beach
:~::::~~~,
Fall ow
o Paved or Graded

o
A
500 1000 1500 Feet
i

-:-::-::c=--==-=::-c--------------------- Pescadero Marsh Natural Preserve Restoration Assessment/202117


SOURCE: ESA
Figure 4
Water Quality Station Locations
I. Introduction

oxygen (saturation and percent), conductivity, specific conductivity, and salinity. On one
occasion we also sampled for pH, using a Hanna Instruments, pHep pocket pH meter. We
sampled for the presence and concentration of hydrogen sulfide in the water column on one
occasion, using a Hach model HS-C test kit. ESA also trained DPR personnel in the use
of this kit, and they conducted additional testing for hydrogen sulfide. Water quality
monitoring results are included in Appendix E and discussed below.

Water temperature was continuously monitored at six locations (Figure 4) during 2002,
using Onset Corp. HoboTemp temperature monitors placed within a clear plastic capsule
provided by the same manufacturer and weighted and tied to stay in the position in which
they were deployed. One meter was lost in the field before its data could be retrieved.
Another meter was re-deployed after data retrieval to maintain a continuous record through
May 29, 2003. We also monitored air temperature at one location using the same
equipment. The temperature monitors recorded a reading every 36 minutes. Temperature
monitoring results are discussed below.

The low levee around the western edge of North Marsh was surveyed using an autolevel
and rod in July, 2002, to ascertain the elevation at the levee breach that we had observed
during field reconnaissance. The elevation was tied to benchmarks placed during the 1987
cross section survey and a United States Geological Survey (USGS) benchmark near the
intersection of Pescadero Road and State Highway 1.

Tide gates and culverts installed as part ofthe enhancement projects of the 1990s were
inspected in 2003 as to operating condition and general condition.

We compiled and analyzed data from several public sources, including streamflow data
from the USGS stream gauge on Pescadero Creek; National Oceanic and Atmospheric
Administration tide predictions and buoy data; and rainfall records from the National
Weather Service. In addition, we compiled and analyzed airphotos from various sources,
including Department of Parks and Recreation files and the U.C. Santa Cruz library.

C. Changes from the Original Scope of Work


ESA's original scope of work with DPR included limited sampling of the Marsh for steelhead and
other aquatic organisms. We were unable, however, to obtain a permit for capture of steelhead, a
federally listed threatened species, in time to conduct the work. Instead, we have inferred the
likelihood of steelhead utilization of areas of the Marsh through observation and analysis of
physical habitat characteristics, and also from past studies (especially Smith, 1987). Similarly, we
did not survey for presence or abundance of other species of concern, including California red-
legged frog, tidewater goby, and San Francisco garter snake, but we did observe current habitat
conditions and reviewed past studies (especially Smith and Reis, 1997), to ascertain the
likelihood of their presence.

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Recommendations for Ecosystem Management March 2008
I. Introduction

2003 local fishermen, working with us under permits from Department of Parks and Recreation
and the National Oceanic and Atmospheric Administration - Fisheries, as well as Department of
Parks and Recreation personnel, observed several hundred dead steelhead smolts along lower
Butano Creek. The fishermen collected several samples" and submitted them to the U.C. Davis
Fish Pathology Laboratory for autopsy under the direction of Prof. Ron Hedrick. Autopsies
revealed no viral, bacterial, or parasitic basis for death, and Dr. Hedrick recommended exploring
environmental causes.

Following completion of field studies for this report, Rebecca Sloan, a State Parks intern and San
Jose State University graduate student, conducted a 16-month study in Pescadero Marsh to
characterize conditions that could contribute to the fish die-offs (Sloan, 2006). Sloan monitored
eight Marsh stations for water quality, including dissolved oxygen (DO), salinity, temperature,
hydrogen sulfide, ammonia, nitrate, phosphate and nitrite, vegetation and phytoplankton
production, surface wind speed and sediment characteristics. Monitoring included continuous
readings taken before, during, and after two successive sandbar breaches (in 2004 and 2005) .
..Sloan found tha law disso ed ox ~_ concentratiens in bottom-water were-pervasive in-th
Marsh after sandbar formatio and mougfwutJ ih - water eelemn . e da s followin -the sandbar
-breachcand-she also ound-eoneentratiens ef-hydregen suUide~fl the b0tt@rrl wateran the lagoon
-and-Butane ehanrre'l. he-eenelueles-that-Peseadere Mars expenences eutroplIi1:atton-a e. +as-
tratificatie ,leadirrg-to-hypo-xic-anChnroxi-c-cona.itions-amllre-f-ormatiu-n-<yf-hydrogen s -fioe;-
.both-ef-whit' a c"Ontribut~t the fcishdie-@-ff~;low s'tlmmer=streamflows~flflear-to-contribute
to these-eorrditicns-e-r'

4 Thanks to Steve Sims, Tim Frahm, and John Fowler for their assistance in this endeavor.

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Recommendations for Ecosystem Management Mard12008
I. Introduction

In the discussion of current conditions and recommended future actions below, we discuss areas
of the Marsh where anoxic salt lenses and hydrogen sulfide were detected both by us and by other
parties between 2002 and 2004. Sloan's findings are not, however, included in the discussion
below. We also present preliminary recommendations for actions that could be considered for
reducing circulation of anoxic and hydrogen sulfide-tainted water following sandbar breaching,
should either of these theories prove correct. It should be pointed out that any such actions would
be premature prior to State Parks obtaining a more thorough understanding of the cause of the
periodic fish die-off and analysis of the consequences of these actions.

D. Adaptive Management
Adaptive management is an approach to natural resource management that requires strategies that
are succinct and consistent enough that their successes and failures at a natural systems level can
be measured, and as a result of those measurements, the strategies can then be systematically
modified.

In the discussion below of individual areas of the Marsh, recommendations for specific
management actions are coupled with recommendations for monitoring and evaluating the
effectiveness of these actions, if they are implemented. Where appropriate, specific parameters or
conditions are noted that, if detected, are indicative of undesirable conditions requiring further
evaluation and possibly a shift in management strategies or goals.

The adaptive management methods have been developed with an eye toward simplicity and
economy. Many of the specified monitoring tasks can be accomplished by DPR interns or by
volunteers, and most require minimal data processing or interpretation.

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Recommendations for Ecosystem Management March 2008
Pescadero Marsh Restoration Assessment 1202 J J 7
SOURCE: ESA
Figure 5
Pescadero Lagoon:
1915 (top) and 2002 (bottom)
I. Introduction

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Recorrmendations for Ecosystem Managerrent March 2008
CHAPTER II
Review of the 1990 Enhancement Plan

The Pescadero Marsh Natural Preserve Hydrological Enhancement Plan (Enhancement Plan) was
prepared by Philip Williams & Associates (PWA), and completed in August, 1990 (Williams,
1990). The Enhancement Plan is based on studies of Pescadero Marsh conducted by PWA, DPR
personnel, and Dr. Jerry Smith of San Jose State University in the middle 1980s (Swanson, 1987;
Smith, 1987), and with reference to earlier studies of the Marsh (Curry et ai, 1985; Osterling,
1987; Viollis, 1979).

The overall goal of the Enhancement Plan was to "manage the preserve to be as natural a system
as possible and to be a good neighbor" (Williams, 1990). The specific goals and objectives bear
repeating verbatim in this report, and include:

1. Restoration and management of the wetland should be carried out on an "ecosystem


approach" to the degree possible, given land use constraints on adjacent lands and in the
upper watershed. Restoration and management should not be carried out on a single species
basis but should consider a sustainable, functional wetland system as the primary goal.

2. Restore the wetland using techniques that allow for long-term, low-cost, and low-technology
maintenance. Attempt to restore the wetland to conditions that would have existed today had
historical human activities not occurred to accelerate sedimentation. Assume the target era of
1928-1941.

3. Develop solutions that will reduce or eliminate the need to manage lagoon water levels for
the purpose of protecting agricultural lands from flooding or from manipulating water levels
for salinity control within the lagoon. Maximize summer and fall water levels in the lagoon
and wetland to optimize wetland and aquatic habitat values in the marsh.

4. Restore full, unrestricted tidal inundation to areas of existing and historic wetland to the
degree possible, including restoration of historic sloughs and tidal channels. Remove interior
levees not needed for flood control.

5. Restore historical sediment dynamics in Pescadero and Butano Creeks. Relocate deposition to
historic floodplain areas away from the marsh and lagoon.

6. Consider the impacts of various restoration and/or flood control alternatives on the habitat of
listed endangered species, specifically the San Francisco garter snake and other sensitive
species, in light of future impacts to existing conditions and continued sedimentation,

Pescadero Marsh Restoration Assessment and 13 ESA/202117


Reconrnendations for Ecosystem Managerrent March 2008
2. Review of the 1990 Enhancement Plan

expansion of undesirable plant species, undesirable water level management, and other
system-wide management problems.

7. For vegetation management:

a. Eliminate and control exotic vegetation within the wetland or encroaching into the
wetland boundaries.

b. Manage vegetation to replicate historical vegetation patterns in the wetland.

8. Co-exist with adjacent agricultural land uses by:

a. Providing flood control for adjacent agricultural lands while preserving, restoring, or
enhancing wetlands and natural resource values on DPR land. Evaluate flood control
alternatives on a cost-benefit basis and consider a land acquisition alternative compared
to construction and maintenance of structures and facilities.

b. Isolating the hydrologic functions of wetlands from adjacent agricultural lands as much
as possible. Consider acquisition as well as structural options.

c. Eliminating direct agricultural runoff from entering the marsh or the streams within the
Natural Preserve'S. Work with local Agricultural Advisory Committee to investigate a
drainage control system.

9. Reduce to an acceptable level flooding of Pescadero Road bridge at Butano Creek through a
cooperative design and construction effort by DPR and San Mateo County. Preliminary
consideration should be given to establishing a stable channel, an adequate bridge crossing,
and sedimentation management.

10. To the extent possible, consider restoration and management alternatives which minimize
channel maintenance requirements and disruption, and maximize flood control benefits for
the adjacent agricultural land and the Pescadero community.

11. Institute a management plan to coordinate and consolidate maintenance efforts in the marsh
with those in the stream channels and watersheds. Plan management response to extreme
hydrologic events, such as major floods and resultant sedimentation and debris accumulation
or drought.

12. Provide an interpretive program for public use, including an interpretive center and trails.

13. Be consistent with the Local Coastal Plan.

5 Presumably this should have been stated as ... "streams within the marsh."

Pescadero Marsh Restoration Assessment and 14 ESA/202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

The Enhancement Plan also lists three constraints to the realization of these goals, which largely
shaped the recommendations included in the Enhancement Plan:

1. The need to maintain habitat of endangered species constrains the basic goal of managing the
preserve to be as natural a system as possible. For example, the San Francisco garter snake
now uses the artificial levees in Pescadero Marsh for basking ... , and the snake feeds largely
on frogs that live in fresh rather than brackish water marsh. Both these factors restrict the
removal of artificial levees, and require that there be no net loss of fresh water marsh.

2. The need for a rapid conversion of the lagoon fromibrackish to fresh water after the mouth
closes constrains the restoration of the historic tidal prism of the lagoon. It is desirable that
the mouth of the lagoon close before flow in the stream gets too low to effect a rapid
conversion of the lagoon. Because dry season flows are now reduced by upstream diversions,
this occurs earlier in the year. If the historic tidal prism were restored, this could keep the
mouth open too far into the summer.

3. Federal and state regulations apply to DPRjust as they apply to anyone else. For example,
DPR will need to get a federal permit to dredge Butano Creek.

The second point requires elaboration. Smith (1987, pp. 15-16) notes that the period of
conversion from saltwater to freshwater in the lagoon following sandbar formation is a time of
low biological productivity. Smith states that invertebrate populations decline precipitously
during the time of transition. As previously discussed, during the transition the water column
stratifies, and a saltwater lens forms at the bottom of the deeper portions of the lagoon, in stream
and slough channels, and in ditches. This saltwater lens quickly becomes anoxic, and provides
conditions for formation of hydrogen sulfide in the substrate and in the water column. Beck
(2003, pp. 3-4) describes this process in some detail. The second constraint in the Enhancement
Plan is based on the desire to maintain favorable conditions in the Marsh for various organisms,
including steelhead, during times of sandbar closure.

The 1990 Enhancement Plan (Williams, 1990) included six major projects elements in its
"Preferred Alternative" to address hydrologically and biologically distinct areas ofthe Marsh:
North Pond - North Marsh; the Butano marshes; the Delta marshes; Butano Creek, and the
Pescadero and Butano Creek riparian corridors. These project elements will be reviewed in the
following chapter.

Pescadero Marsh Restoration Assessment and 15 ESA 1202117


Recommendations for Ecosystem Management Mard12008
2. Review of the 1990 Enhancement Plan

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Pescadero Marsh Restoration Assessment and 16 ESA1202117


Recorrmendations for Ecosystem Managerrent March 2008
CHAPTER III
Results: Historical Changes, Current
Conditions, and Recommendations

This chapter presents the results of our field surveys, review of past studies, including
recommendations contained in the 1990 Enhancement Plan and the history of their
implementation, and compilation of data from other sources. For each area of the Marsh we also
discuss results, provide recommendations for additional study, and where appropriate, provide
preliminary recommendations for future management policies or actions. Where management
actions are recommended, a monitoring and adaptive management program is presented for
assessing the results of actions, should they be implemented. This section is arranged by the
named geographic areas within the Marsh (Figure 2).

For each area of the Marsh, we provide information on pre-disturbance conditions, gleaned
primarily from our own and other researchers' interpretation of two historic documents: an 1854
map (Figure 6) of the Marsh produced by the U.S. Coast Survey (U.S. Coast Survey, 1854), and
an airphoto mosaic from 1928 or 1929 (referred to as the "1928 airphoto") (Figure 7). Historical
changes are interpreted from 1941, 1956, 1986, and 2002 airphotos (Figures 8, 9, 10, and 11);
from oral and documentary histories compiled by Albion Environmental Inc. (as a subcontractor
to Environmental Science Associates under a separate contract with DPR); from other
documentary sources; and from the interpretations of other researchers.

A. North Pond and North Marsh


North Pond and North Marsh are within the area to the north and east of the Pescadero Creek
right banks levee. This includes North Pond, the channel connecting North Pond to Pescadero
Creek, and North Marsh.

1. Pre-Disturbance Configuration of North Pond and


North Marsh
The 1854 U.S. Coast Survey map of Pescadero Marsh (Figure 6) indicates that, at that time, North
Pond and North Marsh were already somewhat isolated from Pescadero Creek and the rest ofthe
Marsh. The map shows an area of higher ground (indicated by the symbol for upland vegetation)
on the right bank of Pescadero Creek from the upper (eastern) limit of North Marsh all the way \

6 Right bank and left bank are relative to an observer facing downstream.

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Recommendations for Ecosystem Managerrent Mard12008
___________________________________ Pescadero Marsh Restoration Assessment /202117
SOURCE: Williams, 1990
Figure 6
U.S. Coast Survey Map of Pescadero Marsh, 1854
;:SO~U:R:::C::E:-:
-=O::P=R---:------------------------- Pescadero Marsh Restoration Assessment /202117
Figure 7
Aerial Photograph: 1928
':SO::U-::R::-::C::E:-:
-=O-=PR::-------------------------- Pescadero Marsh Restoration Assessment /202117
Figure 8
Aerial Photograph: 1941
Pescadero Marsh Restoration Assessment /202117
SOURCE: DPR
Figure
Aerial Photograph: May 2 ,1956
Pescadero Marsh Restoration Assessment /202117
SOURCE: DPR
Figure 10
Aerial Photograph: March 26, 1986
S;'O;:;:U~R~C~E;::-:~D;::-P:R::----------------------------- Pescadero Marsh Restoration Assessment /202117
Figure 11
Aerial Photograph: 2002
2. Review of the 1990 Enhancement Plan

down to the sand dune hook that still extends inland and forms the northern boundary of the
present-day lagoon (as well as the northern abutment for the Highway 1 bridge). The map shows
a road running along this higher ground from about the area of Nunziati Hill all the way down to
the sand dune hook.

Whether this high ground occurred naturally as a natural levee of Pescadero Creek, as suggested
by Curry et al (1985, p. 44) and Williams (1990, p. 9), or whether there was an early effort to
raise the level of this area to provide access to the beach is unknown. It would appear that the
purpose of the road was beach and marsh access only, however, since the road ends at the sand
dune hook, and another road, more or less along the alignment of the current Stage Road, is
visible and was presumably the main route north (as it was until the construction of Highway 1).

North Marsh is shown as wetland on the map, with ponds and channels similar to those seen
today. North Pond itself is marked on the map as "Pond," approximately in its current
configuration. At the northern end of North Pond, an area of wetland extends to a low point in the
dunes, at about the current location of the northernmost parking lot for the State Beach. Another
low point in the dunes occurs at about the mid point of North Pond. Curry et al (1985, pp. 39-40)
note that North Pond is in fact a lagoon, and that prior to construction of State Highway 1 (which
was completed in 1941) high surf would occasionally overtop the beach and flow via the low
northern point into North Pond. North Pond is referred to by Duarte (2002) as "Salt Pond."

2. Changes to North Pond and North Marsh


The 1928 airphoto (Figure 7) shows few changes in North Pond and North Marsh from the 1854
map. The eastern most portion of North Marsh has been diked and converted to agricultural use.
The remainder of North Marsh, however, still appears as a mosaic of ponds, channels, and
vegetated flats, and is still connected to North Pond and thence to the beach via the northern inlet
to North Pond. The road along the "natural" levee on the right bank of Pescadero Creek is visible
on the airphoto as well. Also of note is an inlet or channel extending from the tip of the sand dune
hook inland several hundred feet, and from which several distributary channels flow into
Pescadero Creek just above its confluence with Butano Creek (in the vicinity of the current
location of the six large culverts).

In the 1941 airphoto (Figure 8), major changes have occurred. Newly constructed Highway 1
actually appears to have been built through the western edge of North Pond, severing a small
portion of the pond (the low spot that is now immediately south of the parking lot). According to
Curry et al (1985, pp. 39-40), construction of the Highway 1 berm, and later the northern beach
parking lot, effectively blocked any waves from entering North Pond, thus preventing periodic
flushing of water and sediments from the pond. Also in the 1941 airphoto, the levee along the
right bank of Pescadero Creek has been raised, and a ditch has been excavated along its northern
edge, presumably both for drainage for the diked-off area, and as a source of fill material for
raising the levee. In the photo the ditch is filled with water. There is also a channel from the ditch
to the inlet channel noted above (confirmed on the 1955 San Gregorio USGS 7.5 minute Quad).
According to a 1946 description ofthis arrangement, this channel was gated to enable drainage of

Pescadero Marsh Restoration Assessment and 24 ESA/202117


Recommendations for Ecosystem Managerrent March 2008
2. Review of the 1990 Enhancement Plan

North Marsh into the lagoon, and passed through a culvert beneath the levee (Shapovalov, 1946).
The berm that separated North Pond from North Marsh may have been constructed by 1941, and
a smaller ditch can be seen cutting across the western edge of North Marsh. There is not,
however, the appearance of North Marsh having been tilled, except the easternmost portion,
which had already been tilled in 1928. Duarte (2002, p. 14), states that the Pescadero Creek right
bank levee had been there since he was "a kid" - he was born in 1930 - and that the North Marsh
area was used mostly for cattle, with some farming at the upper (eastern) end.

By the mid 1940s, a dirt road ran along the northern margin of North Marsh, and connected with
the newly constructed State Highway 1 (Shapovalov, 1948). The landowner for this part ofthe
marsh, Mr. Fabro Donelli, rented North Pond to the HalfMoon Bay Duck Club during hunting
season (ibid).

The 1956 airphoto (F igure 9) shows the road, as well as an expanded area of cultivation in North
Marsh. The tilled area now encompasses the entire eastern end ofN orth Marsh, and extends in a
narrow strip wes tward about as far as the confluence of the two creeks.

3. North Pond and North Marsh in the 1980s


By the time of the 1980s surveys, North Pond was still separated from North Marsh by a berm or
levee at the southern end ofthe pond, and from the ocean by the Highway 1 berm. North Marsh
itself was completely separated from the lagoon by the Pescadero Creek right bank levee. A
drainage ditch ran around most of North Marsh, and connected both to the lagoon and to North
Pond through 10" culverts (Smith, 1987, p. 7). Curry et al (1985, p. 39) warned that the fate of
North Pond was to be filled by sediment from hills lope erosion, as the pond had no way of
flushing.

Smith (1987, p. 7) noted that the small culverts between the lagoon and North Marsh, and
between North Marsh and North Pond, conveyed water into these areas from the lagoon when the
water level reached about 2.7 feet (NGVD -29), after formation of a sandbar. Smith also noted that
flood waters in February 1986 topped the Pescadero Creek right bank levee and flooded North
Marsh, which then drained slowly to the culvert level by June, before beginning to fill again after
a July sandbar closure (ibid, p. 7). Smith noted that: "North Marsh always retains considerable
water under the present levee arrangement, while other marshlands within the system ... are
completely drained when the sandbar is open." Smith further noted that isolating North Marsh
and North Pond from the lagoon shortens the time for conversion of the lagoon from salt to fresh
following sandbar closure, a condition he considered favorable for water quality and biological
productivity in the main lagoon area. In addition, Smith pointed out that the small culvert into
North Marsh from the lagoon was effective in reducing lagoon water levels, and thus preventing
or at least delaying flooding of agricultural fields during sandbar closure (ibid).

Because the elevation of the small culvert was 2.7 feet above mean sea level (hereafter expressed
as +2.7 ft msl) (NGVD-29), it siphoned relatively fresh surface water into North Marsh and North
Pond. Smith noted salinities in North Pond and North Marsh of2-7 parts per thousand (ppt) with

Pescadero Marsh RestolBtion Assessment and 25 ESA1202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

little stratification (much lower than values found in the lagoon proper), and that the culvert
between the two areas resulted in gradual equalization of both water level and salinity between
the two bodies when the sandbar was in place (Smith, 1987, p. 9).

Smith found abundant growth ofpondweed (Potamogetonfoliosus) in North Marsh, and dense
phytoplankton blooms in North Pond, both of which contributed to extreme diurnal fluctuations
in dissolved oxygen levels, but which also provided the basis for a large population of
macroinvertebrates, including an abundance of shrimp (Neomysis sp.) in North Marsh (Smith,
1987, pp. 11-12, 15). Smith also found steelhead in 1985 and 1986 in North Marsh, apparently
having come through the culvert or over the levee in a flood. Smith stated that, "the fish had
grown to over 300 mm (standard length) on the incredibly abundant invertebrates in the flooded
marsh, but mid-summer temperatures and low oxygen levels probably killed any steelhead
present" (Smith, 1987, p. 19). In addition to steelhead, Smith found a relative abundance of
tidewater goby in North Marsh and North Pond (though he noted the suboptimal substrate
conditions for the species). He noted that North Marsh was heavily utilized by feeding herons and
egrets, and provided nesting habitat for waterfowl.

In their surveys during the winter, spring, and summer of 19897, Jennings and Hayes found no
evidence of California red-legged frog using North Pond (Jennings and Hayes, 1990, pp. 7-8).
They note that the two habitat components that appear to be most important for California red-
legged frog in Pescadero Marsh - deeper water (~0.7 meters) and thick emergent vegetation
close to water level- were absent from North Pond. Furthermore, in August of 1989, Jennings
and Hayes found salinity levels in North Pond were well in excess of those tolerated by adult
frogs/ibid)".

Jennings and Hayes (1990, pp. 8-10) often observed California red-legged frog or heard them
calling over most of North Marsh during breeding season, and they found numerous egg masses
there. Frogs were encountered in the ditch system along the margins of North Marsh, particularly
in sections of the ditch that featured deep water and dense emergents. During the breeding season
(February-April) when North Marsh was flooded, frogs were observed throughout North Marsh,
but were found only in the ditches as the season progressed and the marsh dried out.

Vegetation in North Marsh in the late 1980s and 1990 was mostly pickleweed, with some other
salt marsh species intermixed (see Appendix A).

4 Enhancement Plan: North Pond and North Marsh Element


Preferred Alternative
The 1990 Enhancement Plan featured a North Pond and North Marsh Element that included
several options for future restoration and management of this area of the Marsh. The Preferred

7 Jennings and Hayes note that their surveys in Pescadero Marsh were preceded by three unusually dry winters,
which may have affected the use of the Marsh by California red-legged frog.
8 Jennings and Hayes found adult frogs in salinities from 0.5 ppt to 10.8 ppt in Pescadero marsh, with most sightings
at salinities :s 6.5 ppt. They note that frogs vacated areas where salinities increased above 6.5 ppt as water levels
receded (Jennings and Hayes, 1990, p. 16).

Pescadero Marsh Restoration Assessment and 26 ESA/202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

Alternative, which is described below, was selected because of its ability to increase tidal prism
to better enable the lagoon to flush sediment during the tidal cycle, and to improve water quality
in North Pond, while maintaining relatively freshwater habitat in North Marsh for the benefit of
California red-legged frog and San Francisco garter snake.

The Preferred Alternative involved connecting the lagoon to North Pond and the western portion
of North Marsh. This was to be accomplished by excavating a new channel from Pescadero
Creek, near its confluence with Butano Creek, through the Pescadero Creek right bank levee. At
this point the new channel would connect to the existing channel that ran along the western and
southern edge of North Marsh. The levee between North Pond and North Marsh was to be
removed, enabling tidewater to flow from the upper lagoon through the newly excavated and
connected channels into North Pond, and back. A low levee was to be constructed near the
channel to a height of +5.5 ft msl, to isolate most of North Marsh from tidewater, and to maintain
relatively freshwater habitat in North Marsh. Two sag ponds were to be constructed within North
Marsh, to provide additional breeding and rearing habitat for California red-legged frog.

In order to control tidal flow into North Pond, and particularly to limit the volume of the lagoon
after sandbar closure (so that conversion of the lagoon from brackish to fresh would be as rapid as
possible), six 4-foot gated culverts were to be placed in the breach in the Pescadero Creek right
bank levee, at a base elevation of -1 ft msl (NGVD-29). The gates were to be closed upon
formation of the sandbar at the mouth of the creek, so that fresh water flowing downstream into
the lagoon would not need to spread out into North Pond, and would thus more rapidly convert
the lagoon proper from salt to fresh. A 12" culvert with a slide gate was to be placed at a height of
+4 ft msl connecting from the south side of the six large culverts into North Marsh, to enable
relatively fresh surface water to siphon into North Marsh as the lagoon water level rose after
sandbar formation. A second 12" gated culvert was to be placed above the six large culverts, at a
height of +4.5 ft msl (NGVD-29), to enable surface waters to flow from the rising lagoon into the
connecting channel and North Pond, and to provide a means of escape for steelhead that might be
trapped on the North side of the large culverts.

During sandbar closure, water level would eventually equalize between the lagoon, North Marsh,
and North Pond. When this occurred, the gates on the six large culverts would be opened, to
enable North Marsh and North Pond to drain after the sandbar breached.

Two additional culverts were to be placed at the north and east end ofthe low levee, to enable
draining of the North Marsh ditches, if desired.

5. Construction History
The North Pond North Marsh Preferred alternative was constructed during the summer of 1993.
A breach in the low levee protecting North Marsh from tidewater was repaired in 1997 (Swanson,
2001, p. 2). DPR staff report having had trouble operating the slide gates from the first year they
were installed, though attempts were still made to operate them until about the year 2000.
(Seidman, pers. com.[e-mail], 5/20/03).

Pescadero Marsh Restoration Assessment and 27 ESA/202117


Recommendations for Ecosystem Managerrent Mardn 2008
2. Review of the 1990 Enhancement Plan

6. North Pond- North Marsh in 2002-2003


This section describes conditions observed in North Pond and North Marsh during the course of
this study, that is, during 2002 and 2003. Figure 11 depicts the Marsh in 2002.

Condition of Water Works

Six Large Culverts


By the fall of2001, when ESA began working in the Marsh, the six large culverts were already
showing signs of deterioration. DPR staff stopped operating the slide gates sometime around
2000, apparently because the screws on the gates were rusting, making them increasingly difficult
to operate. In August, 2002, five of the six gates could still be operated, at least partially, but one
(on the easternmost culvert) was frozen half shut. In addition, the fill structure over the culverts
was eroding, resulting in the loss of at least one half the width of the top of the levee.

By May of2003, much of the fill above the culverts had eroded away, particularly at the north
end of the culverts, and passage over the trail on top of the levee was becoming difficult. The two
middle culverts were broken or separated in the middle, resulting in a bowing up of the middle
section of the pipes, and sinking of their northern ends. The two easternmost pipes were rusted
out just behind their southern, gated openings. While some water was apparently passing through
at least five of the pipes during the tidal cycle, the capacity of the two middle pipes and the
easternmost pipe had declined considerably. During the summer of2003, North Pond was often
empty, with its mudflats exposed. By this time, the reduced capacity of the culverts may have
resulted in less tidal exchange than when the culverts were still intact. This speculative comment
is supported by a State Parks employee who noted that when the culverts were intact, " ... the
water raged like a river out of North Pond and back through the culverts during winter on a big
tidal change."?

The two smaller culverts in the same location, one connecting to North Marsh, the other to the
channel to North Pond, were both open and functioning during sandbar closure in the fall of2002.

The gates on the two culverts between the North Marsh ditches and the connecting channel were
badly rusted in 2003, and could not be operated.

Low Levee
The low levee, which was constructed in 1993, was intended to protect North Marsh from tidal
intrusion, thus resulting in fresher water habitat to benefit California red-legged frog, San
Francisco garter snake, and tidewater goby. The levee was constructed to a height of +5.5 ft msl
(NGVD-29), high enough to prevent overtopping by nearly all high tides. Smith and Reis (1997,
p. 4) report the effective constructed height of the low levee was only +4.7 ft msl (NGVD-29),
and that within months of its completion, it was being overtopped by high tides. In 1997, a partial

9 Personal Communication, Paul Keel, State Parks, December 12,2005.

Pescadero Marsh Restoration Assessment and 28 ESA/202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

breach in the levee was repaired, but by 2001, the levee was again breached along its western
side.

In July, 2002, we surveyed the elevation of the top of the low levee to measure the depth and
extent of the breach, and to identify any other low spots. The lowest point in the breach was
+3.59 ft msl (NGVD-29), at a point 285 feet from the northern end of the low levee. The survey
results are shown in Figure 12, which also indicates several other areas where the elevation of the
low levee is below +5 ft msl (NGVD-29).

7.5,------------------------------------------------------------------.

7+-----------------------------------------------------------+-----~

6.5+-----------------------------------------------------------~----~
I
~
j 6+----------------------------------------------------------4------~
~
e

~ 5.5~~--------------~------------------A.~~~of~--~H>n_+_------~
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..,o.
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~ 5+---~~~~_r_+----------~*7~_+++------------~_h~------------~
..
!!!
iii

4.5+------------4~--------------------------------------------------~

4+-----------~~--------------------------------------------------~

3.5+-~~~~~~~~~~~~~_+~~~~_r~~~~~~~~~+_~~~~
o 200 400 600 800 1000 1200 1400

Distance from North End of Low Levee (Feet)

------------------------------------------- Pescadero Marsh Restoration Assessment 1202117


SOURCE: ESA
Figure 12
Elevation of the Top of the North Marsh Low Levee, July, 2002

On August 8, 2002, on the night of one of the highest tides of the year (0.2 ft lower than the
predicted highest tide of the year), we installed a crest gage to measure the water elevation at the
North end of the low levee, and to see if, at this water level, water would flow through the breach
in the low levee. The next morning, the crest gage reading, corrected to indicate height above
mean sea level (NGVD-29), was +3.65 ft. msl (NGVD-29), or 0.05 ft. above the surveyed low
point on the low levee. However, inspection of the breach indicated no signs of the levee having
been overtopped. This may be because vegetation between the connecting channel and the low

Pescadero Marsh Restoration Assessment and 29 ESA1202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

levee dampened the flow of water sufficiently to prevent overtopping. In any event, it appears
that only the highest of the high tides would overtop the low levee breach, and then probably only
for a short time.

Operation of Water Works


As described above, the 1990 Enhancement Plan called for closure of the six large culverts within
a few days of formation of the sandbar. This would reduce the lagoon volume, by isolating North
Pond from the lagoon, and thus enabling a more rapid conversion of the lagoon from salt/brackish
to brackish/fresh water. Once the lagoon level reached the height of the small culverts, relatively
fresh surface water would begin to flow into North Marsh and into the channel to North Pond.
Eventually the water level would equalize on either side of the culverts, though the water on the
north side would be fresher and less stratified than that in the lagoon. Once the lagoon level
equalized with that in North Pond and North Marsh, the tide gates were to be open, to allow the
drainage of North Pond and North Marsh (to the level of the low levee) when the sandbar
breached, and to enable, once again, tidal exchange in and out of North Pond.

With five of the culverts left in the open position, and the sixth partially closed, at least some tidal
exchange in and out of North Pond has been maintained during times when the mouth of
Pescadero Creek is open. The condition of the culverts, however, seems to be restricting flow into
the channel leading to North Pond. For example, we observed that, after the turn of the high tide,
when flow was already out to sea at the Highway 1 bridge, there was still flow northward through
the culverts, indicating that the water level had not equalized on either side of the culverts. This
condition was further observed after the winter of 2002-2003.

After sandbar formation on September 17, 2002, water level rose slowly in both the lagoon and in
North Pond. On October 24, 2002, about one month after sandbar formation, we observed water
overtopping the breach in the low levee at a depth of3-5 inches. In addition, water was observed
on this date flowing through the small culvert into North Marsh. On this day, the water level
reading at the data logger by the Butano levee footbridge was +4.05-4.06 ft msl (NGVD-29)
(Figure 13).

Pescadero Marsh Restoration Assessment and 30 ESA 1202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

~ s ~ ~ si;j
1.'! 1.'!
~ ~
1.'!
~ ~ ~ ~
M

~ ~ ~ ~
a
s ai ~ '" ~ ;; s ~ ~ ~
M ~
Date

---------------------- Pescadero Marsh Restoration Assessment 1202117


SOURCE: ESA
Figure 13
Water Surface Elevation at Station WL, 2002-2003

Water Quality
Water quality was sampled at several locations in North Pond and North Marsh during the
summer and fall of2002. Sample locations included most of those recommended for continual
monitoring by Smith and Reis (1997): stations Cl, C2, C3, El, Fl, F2, SI, and S2 (see Figures 4
and 14-18 and Appendix E). Smith and Reis (1997) report salinity levels during 1995 and 1996,
with some records from 1993 and 1994. The salinity profiles they reported indicate that salinity in
this area, during times when the tide gates at the large culverts were open, changed seasonally,
becoming generally fresher in the winter and more saline in the summer. When the tide gates
were closed, the restoration work was reasonably successful in keeping more saline water out of
North Marsh and North Pond, and allowing fresher surface water to flood these areas gradually.
Except in the connecting channel, which (when the culverts were open) fluctuated from brackish
to saline with the tides, most of the readings indicated a mildly brackish marsh with little saline
stratification through the water column.

Pescadero Marsh Restoration Assessment and 31 ESA1202117


Recommendations for Ecosystem Management March 2008
Dissolved Oxygen at Station C1

16

14
'aE.
C 12
~
e
..
C 10
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8

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0
5/24/2002 6/18/2002 7/13/2002 8/712002 9/1/2002 9/26/2002 10/21/2002 11/1512002 12/10/2002

I-+-surface -+-1 foot deep --.-2 feet deep __ 3feet deep -.-4 feet deep I

Salinity at Station C1

5124/2002 611812002 7/13/2002 8f712002 9/112002 9/2612002 1012112002 11/1512002 12/10/2002


0

10

a.
a. 15
~
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20

25

30

35

I-+-surface -+-1 foot deep --'-2 feet deep __ 3feet deep -.-4 feet deep I

Temperature at Station C1

22

20

~
~
18
"w
4i
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..~
~ 16

'"..
0
14

12

10+---------r-------~--------_r--------~--------~--------r_------~--------~
5124/2002 611812002 7/1312002 817/2002 9/112002 9/2612002 1012112002 11/1512002 12110/2002

I-+-surface -+-1 foot deep --'-2 feet deep __ 3feet deep -'-4 feet deep I
------------------------------------------------ Pescadero Marsh Restoration Assessment/202117 -
SOURCE:ESA Figure 14
Station Cl Water Quality
2. Review of the 1990 Enhancement Plan

o 5 10 15 20 25 30

II
o

\
\
0.5

!
:;;- 1.5
1i
e
c

2.5 -

1 __ Temperature (C) --- DO Concentration (mg/I) Salinity (ppt) I


------------------------- Pescadero Marsh Restoration Assessment 1202117
SOURCE: ESA Figure 15
Station C2 Vertical Profile

Pescadero Marsh Restoration Assessment and 33 ESA1202117


Recommendations for Ecosystem Management March 2008
Dissolved Oxygen at Station C3

14

'. 12
E
i::
0
10

~
8c 8
0
U
c
"'"s;- 6

o
-e
~
~
"0
~
i5

o+-----~------~------~----~------~----~------~------~----~
6/13/2002 7/312002 7/23/2002 811212002 9/1/2002 9/21/2002 10/11/2002 10/31/2002 11/20/2002 12/10/2002

l--sUrface -+-1 foot deep 2 feet deep 3 feet deep -lI!-4feetdeep I

Salinity at Station C3

6/13/2002 71312002 7/2312002 811212002 9/112002 9/21/2002 10/1112002 10/3112002 11/20/2002 1211012002
o

10
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Q.

~ 15
:~
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'" 20

25

30
.-----
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I__ surface -+-1 foot deep 2 leet deep 3 feet deep -lI!-4 feet deep I

Temperature at Station C3

28

26
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24

~
~ 22

a;"
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20
o
~ ~~
~ 18

~'" 16
~
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6/1312002 71312002 7/2312002 811212002 911/2002 9/2112002 10/11/2002 10/31/2002 11/20/2002 12/10/2002

I__ SUrface -+-1 loot deep 2 leetdeep 3 leetdeep -lI!-4 leet deep I

------------------------------------ Pescadero Marsh Restoration Assessment/202l 17


SOURCE:ESA Figure 16
Station C3 Water Quality
Dissolved Oxygen at Station E1

25r--------------------------------------------------------------------,

~ 20+---------------------------------------------~~--------------------------_1
C
o
~
C
m 15+-----------------~~~~--------------------------~~--------------------~
u
c
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s

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5/24/2002 6/1812002 7113/2002 af712002 9/1/2002 9/26/2002 10121/2002 11/15/2002 12110/2002

l-+-sUrface 1 fool deep ..... 2 feel deep """*""3 feel deep I

Salinity at Station E1

5124/2002 6/1812002 7113/2002 af712002 9/112002 9/2612002 1012112002 11/1512002 12110/2002


o

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Temperature at Station E1

35

30

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ai
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co 20
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0

15

10+---------r--------,---------T---------r--------,---------r--------,--------~
512412002 611812002 7/1312002 8f712002 9/112002 9/2612002 1012112002 11/1512002 12110/2002

I-+- surface ~ 1 foot deep --6- 2 feet deep --+f- 3 feet deep I

------------------------------------------------------------------- Pescadero Marsh Restoration Assessment/202l 17


SOURCE:ESA Figure 17
Station El Water Quality
2. Review of the 1990 Enhancement Plan

0 5 10 15 20 25

/
0

~
~
.s::;
a.
c"
2
/
3~-- __ ----------------------------+---------------------------

1-- Temperature 1
4 _

(C) -- DO Concentration (mg/I) Salinity (ppt)

----------------------------------------- Pescadero Marsh Restoration Assessment / 202117


SOURCE: ESA
Figure 18
Station F2 Vertical Profile, November 21,2002

In 2002, however, salinity throughout North Pond and North Marsh was higher than reported by
Smith and Reis. Before the pond in North Marsh completely dried up at the beginning of July,
salinity at station F2 reached 21 parts per thousand (ppt) on June 13 and 32.7 ppt on June 30. The
ditches on the north and south sides of North Marsh (stations F 1 and El - see Figure 17) were
also quite saline during the summer, with readings from 12.1 to 23.7 ppt. The sag ponds (stations
SI and S2) were almost as saline, with readings of 8.6 to 12 ppt in June, increasing to 12.2 to 12.4
after sandbar closure, but before North Marsh (and the sag ponds) began to fill from the
risinglagoon water. After sandbar closure, the entire North PondINorth Marsh area became
brackish to saline, with surface readings in the high teens to low twenties, and readings at greater
depths up to 27 ppt (Figures 14-18). Dissolved oxygen levels dropped and became more
stratified, with anoxic conditions developing in the bottom one to two feet ofthe water column.

Water temperature was monitored continually at station CI, just north of the large culverts, from
late spring through fall of 2002 (Figure 19). Figure 19 is a typical temperature graph for tidal
areas of the marsh, with large diurnal temperature ranges while the mouth of the creek was open,
and a much more limited diurnal range after sandbar formation. The approximately weekly cycle
of peaks in the weeks after sandbar formation is apparently correlated with changes in air

Pescadero Marsh Restoration Assessment and 36 ESA/202117


Recommendations for Ecosystem Management Mard12008
2.Reviewofthe1990Enhancement
Plan

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----------------------------------------------- Pescadero Marsh Restoration Assessment I 202117


SOURCE: ESA
Figure 19
Station C1 Water Temperature

temperature during that time (Figure 20). Note also the temperature peak that corresponds with
the first significant rain event of the year, on November 6, and the subsequent temperature dip
that corresponds with the high surf event on and around November 8, which resulted in a large
volume of cold ocean water overtopping the sandbar and filling the marsh. Beck (2003)
monitored several water quality parameters continuously in the channel between the six large
culverts and North Pond, from May 2nd through December 9,20021 Beck was particularly .
interested in observing the formation of an anoxic layer at the bottom of the water column, and

10 Beck also sampled Butano Creek just below the Pescadero Road bridge, and Pescadero Creek at the Stage Road
bridge, for nitrate and phosphate, on several occasions in the summer of2002. Nitrate levels were consistently quite
low, and phosphate levels were below the detection limit.

Pescadero Marsh Restoration Assessment and 37 ESA/202117


Recorrmendations for Ecosystem Managerrent March 2008
2. Review of the 1990 Enhancement Plan

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------------------------------------------------- Pescadero Marsh Restoration Assessment / 202117


SOURCE: ESA
Figure 20
Pescadero Marsh Air Temperature (at Station XS-11)

selected this location after detecting the odor of hydrogen sulfide gas in the area after the
breaching of the sandbar in 2001. The instrument she installed recorded an abrupt drop in
dissolved oxygen in late November at the level of the sensor (0.7 feet above the bottom
sedimentj.U

11 Beck attributes the increase in salinity detected on November 8th to freshwater input from the first runoff event of
the season, and the subsequent concentration of saline water near the bottom of the water column where the sensor
was located. However, we observed that the high surf of November 8 and the next few days overtopped the sandbar
and introduced a large quantity of ocean water into the marsh.

Beck makes a rough calculation of the amount of anoxic water within North Marsh and North Pond at the time of
the breaching of the sandbar. Her estimate of25 acre feet of anoxic water is based on an assumption of.7 feet of
anoxic water over the entire area of North Pond and North Marsh, a 35-acre area. However, the elevation of most of
North Marsh, as well as the pickleweed flat adjacent to the channel connecting the six large culverts to North Pond,
is well above the elevation of her sensor. Our own spot measurements within North Marsh around this time indicate
much lower salinity and less stratification of the water column than both Beck and we detected in the connecting
channel. It appears that anoxic bottom conditions form only in the deeper channels and ditches, and not on the
inundated flats. Therefore, Beck's estimate of the volume of anoxic water in North Pond and North Marsh is
probably too high by about an order of magnitude.

Pescadero Marsh Restoration Assessment and 38 ESA1202117


Reconmendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

Biological indicators

Vegetation Changes
Two of the 10 vegetation transects, originally established in 1985 by DPR personnel, and
surveyed several times during the late 1980's, are located in North Marsh. ESA personnel re-
surveyed these transects in the summer of2002 to determine current species composition and to
compare this with the earlier surveys. The results are described in detail in Appendix A, and
summarized here.

North Marsh is a characteristic pickleweed salt marsh as sampled by Transects T7 and T8, and
has shown little change since the earlier surveys. Transect T7 has remained with relatively
monotypic pickle weed cover (90 and 89% in 1990 and 2002, respectively; earlier monitorings
were over 80% pickleweed and open water or unidentified dead material). Transect T8 is slightly
more diverse, with pickleweed ranging between 53-59% in the various surveys, and other salt
marsh species, principally alkali heath (Frankenia salina) and marsh gumplant, accounting for
most of the remaining cover. Of concern in the 2002 monitoring is the appearance of poison
hemlock (Conium maculatum), an invasive weed, at 6% cover. No other invasive weeds were
recorded in the North Marsh transects in earlier surveys or in the 2002 survey.

Habitat for Species of Concern

California Red-Legged Frog


The main indicator we used to determine habitat suitability for California red-legged frog
breeding was the presence of slow water that persists from winter through mid summer, with low
to moderate levels of salinity. Jennings and Hayes (1990) indicate that water at least 0.7 meters
deep, and thick emergent vegetation close to water level, are important habitat components. They
note that salinity above 5 ppt causes deformities and death in embryos, and that during their 1989
surveys, adult frogs in Pescadero Marsh vacated areas as salinities increased above 6.5 ppt
(though adult frogs were observed in salinities up to 10.8 ppt) Smith and Reis (1997) found
extensive use of North Marsh by California red-legged frog in 1996, but cautioned that the
inability to flush North Marsh with fresh water and the breach in the low levee threatened to
make this area too salty for breeding and rearing success, as eggs do not tolerate salinity above
4 ppt, and tadpoles do not tolerate salinity above 7.5 ppt (Smith and Reis, 1997). Jennings and
Hayes (1990) recorded surface salinities between 4.0 and 4.8 ppt in March, 1989 in North Marsh,
and much higher salinities-from 10.4 to 20.5 ppt in August, 1989. Water quality monitoring
conducted for the present study indicates that North Marsh was too salty for red-legged frog
breeding and rearing. Furthermore, in 2002 and again in 2003, North Marsh dried up, except for
the ditches and sag ponds, by early summer. Based on observations of salinity levels in the North
Marsh area, it appears that the quality of red-legged frog breeding habitat during this study was
poor.

Pescadero Marsh Restoration Assessment and 39 ESA/202117


Recommendations for Ecosystem Managerrent March 2008
2. Review of the 1990 Enhancement Plan

San Francisco Garter Snake


McGinnis (1987,2002) provides an evaluation system for potential feeding habitats for the San
Francisco garter snake in the San Mateo County area. In this system, the most important
indicators of feeding habitat are impounded perennial fresh water; dense reed-shrub cover
throughout a marsh or in a wide band around a pond edge; presence of both Pacific tree frog and
California red-legged frog; and lack of competitive garter snakes. The relatively high salinity
levels observed in North Marsh during this study indicate that, at that time, the quality offeeding
habitat for San Francisco garter snake was poor.

Tidewater Goby
Tidewater goby prefer calm, mildly saline water with sandy substrate. Increased tidal circulation
in North Pond and in the channel leading to it have probably reduced the utilization ofthese areas
by tidewater goby, at least in the absence of a sandbar (Smith and Reis, 1997, p. 12). Smith and
Reis (ibid) found Tidewater goby in North Marsh after it flooded in November, 1995, and in open
water and the north ditch in North Marsh the following spring.

Steel head
The channel to North Pond, and perhaps North Pond itself, may be utilized as foraging habitat by
steelhead. We observed fish on the north side of the large culverts, but could not identify them. It
is possible that steelhead are now able to use North Marsh as a feeding ground when it is flooded,
and still escape into the lagoon when conditions deteriorate. However, this possibility is
predicated on leaving the culvert gates open during sandbar closure, which is contrary to their
prescribed use.

As discussed above, anoxic conditions and hydrogen sulfide form in the channel between the
large culverts and North Pond. The observed fish die-offs of2001, 2002, and 2003 did not seem
to occur in this area.

7. Discussion
The North Pond and North Marsh enhancement projects may have resulted in a decline in habitat
for species of concern. This is due both to the design of the projects, and to their deterioration
since they were installed. Of particular concern are the high salinity levels observed in North
Marsh, and the consequent poor habitat quality for California red-legged frog in this area.

The primary purpose of the six large culverts and the connecting channel to North Pond was to
increase tidal prism and to enable sediments to flush from North Pond. While tidal prism has
increased somewhat, the current condition of the culverts reduces their conveyance capacity.
While we did not survey the elevation ofthe bed of North Pond, it appears to be quite shallow,
and has a soft mud bottom, indicating little if any scour in recent years (DPR staff indicated that
scour visibly occurred in North Pond soon after construction of the connecting channel).

Pescadero Marsh Restoration Assessment and 40 ESA/202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

this area, and enable ponding of water in North Marsh. 12 Floodwaters would enter North Pond
and North Marsh relatively frequently; calculation of the height of bankfull flow in Pescadero
Creek can be used to estimate flood frequency. Further upstream, the levee could be 0.5 to 1.0
feet lower than the height further downstream: the attenuation ofthe high tide elevation further
upstream, plus the gradient of the stream would still prevent high tides from overtopping the
levee, and a lower elevation would increase the frequency of flooding from Pescadero Creek high
flows. 13This would create a fresh or mildly brackish marsh, which in some years may stay
flooded year-round, but in any event would gradually become saltier over the course of the season
with evaporation. In large floods, receding floodwaters would flush accumulated salts from North
Marsh. During lagoon formation, rising lagoon water would also spill over the new low levee into
North Marsh and North Pond. Because of the elevation of the levee, this would be mildly
brackish water. Lowered portions of the levee may need to be armored to prevent erosion during
flood recession.

The intended result would be to create or enhance breeding and rearing habitat for California red-
legged frog, at least during some years, and to improve conditions for tidewater goby, also at least
during some years. Expanding the breeding range of red-legged frog could also expand habitat for
San Francisco garter snake, if frog abundance is currently a limiting factor for the snake.
Vegetation on the new low levee and the remaining portions of the existing low levee (see
recommendation e, below) may have to be managed in order to provide a diversity of habitat
types. Steelhead juveniles and smolts would be able to pass over the low levee during floods and
during lagoon high water and utilize this area for foraging, but would also be able to pass back
out to the main lagoon at sandbar breaching or while lagoon water level is still high, with some
expectation that fish may become trapped.

c. Determine whether gullies above North Pond are contributing to the sedimentation of North
Pond, and if so, control gully development with the intent of reducing the rate of sedimentation.

d. Revisit the recommendation of Curry et al (1985) to re-establish a connection between North


Pond and the ocean. Curry et al had recommended a box culvert beneath Highway 1 that would
enable unusually high surf to overtop the low point in the dunes and enter North Pond. This may
encourage flushing of North Pond and re-establish it as a functional lagoon, and may at times
result in Pescadero Creek flowing to the sea through North Pond. A bridge or causeway over the
northern part of the dune field may be a more practical long-term solution, as a box culvert may
tend to plug with sand.

e. Remove a section of the low levee separating North Marsh from the channel connecting North
Pond to the large culverts, to enable free circulation of water throughout this area during floods
and high lagoon levels. The remaining part of the low levee could be left to provide pedestrian

12 Curry et al (1985, p. 90), recommend minimum dimensions for levee breaches to be 280 feet wide and 2-4 feet
below the level of the area being drained. We do not recommend lowering the levee below the level of North Marsh
(about +4-5 feet msl), but rather maintaining a minimum level across the levee several feet above the elevation of
North Marsh
13 Deployment of a water level logger at Turtle Bend during spring and summer with open sandbar conditions would
determine high tide levels at the site of the recommended levee lowering.

Pescadero Marsh Restoration Assessment and 42 ESA1202117


Recorrrnendations for Ecosystem Management Marcl12008
2. Review of the 1990 Enhancement Plan

Operation and maintenance of the tide gates, and keeping the low levee in good repair have
proven to be impractical. More fine-tuned manipulation of the system using the gated culverts on
the North Marsh ditches is no longer possible, given the condition of the gates.

8. Recommendations
Desired Conditions
The desired condition for North Marsh and North Pond is a self-maintaining area that provides a
diversity of habitats, including habitat for the species of concern that inhabit the Marsh, and that
vary seasonally and over time in response to changing conditions. Based on consistent
observation over time of pickleweed as the dominant species in North Marsh, it is likely that the
historic condition of this area is as brackish to salt marsh. Variations in salinity levels observed
over time indicate that, at least since the major alterations were made to North Marsh hydrology
beginning in the early part of the zo" century, and perhaps before, it is likely that habitat for the
species of concern varied from year to year depending on rainfall, flood regime, lagoon level, and
perhaps other factors.

The potential benefits and perils of allowing steelhead juveniles and smolts to utilize North Marsh
as spring and summer feeding areas should be further evaluated. This area should also provide
habitat for a variety of birds.

Recommendations for Further Study and Actions


The following preliminary recommendations would require further analysis both to determine
their ability to meet long-term Marsh management goals, and to understand fully their benefits
and potential adverse impacts.

a. Study options for modifying the six large culverts and the connecting channel between the
culverts and North Pond. Options might include:

1. Repair the culverts and levee and replace the gates using materials and designs that will
withstand the rigors of the brackish water environment without extensive maintenance.

2. Remove the six large culverts, and either fill the channel between the culverts and North
Pond completely, or leave sections of the channel that will act as a series of sag ponds.

3. Replace the culverts with a bridge.

b. In order to mimic the most likely pre-disturbance condition, that is, a natural levee along the
right bank of Pescadero Creek separating the stream channel and lagoon from North Marsh and
North Pond (with no connecting channel), further investigate the possibility ofreconfiguring the
levee and establishing the height of the levee at between +5 and +6 ft msl (NGVD-29). The
height of the levee should be established such that its minimum height would prevent tidal
intrusion into North Marsh and North Pond, but enable overbank flow of Pescadero Creek into

Pescadero Marsh Restoration Assessment and 41 ESA/202117


Recol1111endationsfor Ecosystem Managerrent Mard12008
2. Review of the 1990 Enhancement Plan

access, San Francisco garter snake basking habitat, and greater diversity of vegetation. Spoil from
lowering the levees would be used to fill or partially fill the artificial ditches around the perimeter
of North Marsh, and the artificial channel between Pescadero Creek and the large culverts, in
order to mimic our understanding of the pre-disturbance (1854) hydrology of North Marsh. Spoil
could also be used to fill short sections of the ditches, creating sag ponds with surrounding higher
ground that could be used by California red-legged frogs and San Francisco garter snakes.

g. Consider constructing boardwalks over the low levees to allow year-round access. The
elevation of the boardwalks should be above the typical lagoon water surface elevation of about
+6.5 ft msl, and should be constructed to withstand inundation in occasional floods.

9. Monitoring and Adaptive Management Program for North


Marsh and North Pond
If these or similar actions are implemented, it would be crucial to monitor water quality and water
elevation in North Pond and North Marsh in order to determine the effectiveness of the
implemented actions in creating habitat for special status species. Monitoring should include
monthly sampling throughout the water column for salinity, dissolved oxygen, and temperature.
Water level should also be recorded.

This information should be supplemented with surveys of vegetation and special status species
presence. Repeating the vegetation transect surveys and surveying for California red-legged frog
every 2-3 years is recommended. This area should also be surveyed periodically for bullfrog
(Rana catesbeiana) and yellowfin goby (Acanthogobius flavimanus). Presence of these species
may indicate undesirably low or high salinity, respectively.

B. Butano Marshes
The Butano Marshes include the wetland areas on the left bank of Butano Creek, and bordered on
the south and west by Pescadero Road and the coastal terrace. In current nomenclature, the
Butano Marshes are divided into North Butano Marsh, Middle Butano Marsh, and East Butano
Marsh (Figure 2). North Butano Marsh extends from the footbridge over the breach at the north
end of the Butano left bank levee to the remnants of one of two levees that once extended from
the southwest edge of the marsh to the main left bank levee, at a point called the Triple Junction.
Middle Butano Marsh, the smallest of the three, is the area between the two remnant levees. East
Butano Marsh (sometimes called South Butano Marsh) extends from the second remnant levee to
the alder patch below the Pescadero Road bridge over Butano Creek.

1. Pre-Disturbance Configuration of the Butano Marshes


The 1854 U.S. Coast Survey map of Pescadero Marsh (Figure 6) shows wetland throughout the
same area currently occupied by the Butano Marshes. The high water line in the lower channel of
Butano Creek indicates that the lagoon area may have extended up the creek at this time.
Numerous slough channels snake through the Butano Marshes, including one quite large

Pescadero Marsh Restoration Assessment and 43 ESA 1202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

meandering channel. The map shows the Butano Marshes dotted with several ponds of varying
sizes, and the absence of contour lines indicates a relatively common elevation throughout the
marshes. The symbol for upland vegetation on the 1854 map begins at about the present location
of the beginning of riparian forest along Butano Creek, that is to say, about 2,500 feet
downstream of the Pescadero Road bridge. An earlier iteration ofthe Pescadero Road bridge is
shown on the 1854 map, in about the same location as the present bridge.

2. Historic Changes to the Butano Marshes


The 1928 airphoto (Figure 7) shows the Butano Marshes having essentially the same
configuration as in 1854. The same slough channels and ponds that are depicted on the map can
also be seen in the photo. There is an anomalous color change in the photo at about the dividing
line between the North and Middle Marshes, but no levee construction is evident, and we
conclude that this is a distortion in the image.

In the 1941 airphoto (Figure 8), it appears that East Butano Marsh and perhaps a portion of
Middle Butano Marsh had been leveed and drained, or at least cleared. A roadway (and
presumably also levee) extends along the left bank of Butano Creek from around the Pescadero
Road bridge to about the location of the Triple Junction, then veers 90 degrees to the southwest
and crosses the marsh to the vicinity of Pescadero Road. It appears that the riparian forest
downstream of the Pescadero Road bridge had been cleared. Slough channels are no longer
visible in East Butano Marsh. The main slough channel that meandered through the marshes may
have been connected to the main Butano Creek channel where it swings east and the creek swings
west.

The 1956 airphoto (Figure 9) shows that the northeastern half of both East Butano Marsh and
Middle Butano Marsh had been cleared and that this area was dry. A ditch or levee divided this
area from the southwestern half.

According to Cook (2003), the left bank levee and the two cross-marsh levees were constructed
with a dragline in or around 1960. South Butano Marsh and Middle Butano Marsh were thereafter
used for agriculture or grazing, but North Butano Marsh, though isolated from Butano Creek by
the levees, was never tilled. This information does not, however, agree with our interpretation of
historic air photos, which indicate that levee construction and conversion to agriculture occurred
somewhat earlier.

As part oflevee construction, soil was borrowed along the outboard side of the levee, creating a
ditch that probably runs the entire length ofthe levee, but certainly from the Triple Junction
downstream. When the north end of the levee was breached in the 1980s, this ditch, which is
more than 100 feet wide near this point, connected the creek to the old slough channel that is
shown meandering through the Butano Marshes on the 1854 map and in the 1928 and 1941
airphotos.

Pescadero Marsh Restoration Assessment and 44 ESA/202117


Recorrrnendations for Eccsystem Management March 2008
2. Review of the 1990 Enhancement Plan

3. The Butano Marshes in the 1980s


By the time of the surveys in the 1980s, the Butano Creek left bank levee was still intact, except
for a narrow breach at its north end, in the present location of the footbridge, and a second breach,
constructed in 1985, at the upstream end of the marsh, about 50 feet downstream of the Pescadero
Road bridge (Smith, 1987; Figure 10). The two cross-marsh levees that define the three Butano
marshes were also intact, except for narrow breaches, which were made around the same time
(Curry et al, 1985) Apparently, the breach at the north end of the main levee was sufficiently
narrow to restrict tidal intrusion into the remnant slough channels in North Butano Marsh, but
winter floods were able to enter the Butano Marshes through the upstream breach, and rising
lagoon waters would flood all of the marshes. (Smith, 1987, p. 7).

Smith found dense growth of pondweed (Potamogetonfoliosus) in the Butano Marsh slough
channels in the summer, which he observed was providing foraging habitat for steelhead during
the day and evening, when dissolved oxygen levels were high. (Smith, 1987, pp. 11, 19). Smith
also notes that the salinity ofButano Marsh in late summer was higher than in the rest of the
marsh, though still quite low (by present standards) at 2.0-3.1 ppt.

Jennings and Hayes (1990) observed or heard calling California red-legged frogs only in Middle
and East Butano Marsh, but none in North Butano Marsh. They observed frogs along the edges of
open, deep water pools that were scattered within the dense matrix of emergent vegetation (ibid,
pp. 11-12). They note that, despite the limited circulation through the Butano Marshes at the time,
this area appeared to have the greatest area of high quality red-legged frog habitat within
Pescadero Marsh (ibid, p. 12).

In the 1980s and 1990, vegetation surveys (Transects T1 and T2; see Figure 3) in East Butano
Marsh indicated moderately saline conditions, with characteristic salt marsh plants present,
including pickleweed and marsh gumplant, and with less presence of brackish and fresh water
species than are currently found in this area. The eastern transect in North Butano Marsh (T3) in
the 1980s was composed primarily of pickleweed and other salt marsh species, while the western
transect in North Butano Marsh (T4) was composed primarily offresh and brackish species (bull
tule and cattails).

4. Enhancement Plan: Butano Marshes Element Preferred


Alternative
The Preferred Alternative of the Butano Marsh Element of the 1990 Enhancement Plan included
two parts. Part 1 was partial removal of the Butano Marsh Levees, to restore natural circulation of
water through the marshes. Connecting channels would be excavated to re-connect remnant
slough channels on either side of the cross-marsh levees. However, portions of the levees were to
be left to provide basking habitat for the San Francisco garter snake and, with the addition offoot
bridges, pedestrian access into the Marsh.

Pescadero Marsh Restoration Assessment and 45 ESA1202117


Recorrrnendations for Ecosystem Managerrent March 2008
2. Review of the 1990 Enhancement Plan

The second part of the Preferred Alternative for the Butano Marshes involved additional levee
removal and channel excavation to improve flood conveyance from Butano Creek through the
marshes. This would include the removal of what is described as a small peninsula just
downstream from Pescadero Road, and the lowering of the ground surface elevation in this
location to 8.0 feet. For 150 feet downstream from the Pescadero Road bridge, left bank
vegetation would be managed to maintain a closed upper canopy with little understory vegetation.
This was intended to improve flood conveyance into East Butano Marsh. In addition, the left
bank levee would be removed for 100 feet upstream from the Triple Junction, to increase
overbank flow into South Butano Marsh.

5. Construction History
Part 1 of the Preferred Alternative for the Butano Marshes was completed in 1993. Part 2 was
never undertaken.

6. Butano Marshes in 2002-2003


This section describes conditions observed in the Butano Marshes in 2002 and 2003, and reviews
data presented by Smith and Reis (1997).

Condition of Water Works


The levee breaks and connecting channels excavated in 1993 are still functioning to convey water
from Butano Creek through the marshes. The enlarged breach at the north end ofthe left bank
levee conveys tide water into the ditch that runs along the outboard edge of the levee, and from
there into the remnant distributary channel.

There is still pedestrian access along the left bank levee, from the footbridge to the break
downstream of the Triple Junction. However, as of the summer of2003, the levee, including the
trail, was overgrown with vegetation, and the trail was becoming difficult to pass. The
footbridges over the breaches in the cross-marsh levees were displaced by high water (in 1998),
and have not been replaced, thus preventing access, both for recreation and for maintenance, to
the remaining portions of these levees.

Operation of Water Works


The water works in the Butano Marshes, that is, the levee breaches and excavated channels,
function passively and have required no maintenance.

Water Quality
Water quality sampling at several locations in 2002,2003, and early 2004 (2003 and 2004
monitoring by State Parks personnel) indicate that the Butano Marshes contain fresh water during
periods of high runoff, but that during the times when there is no sandbar, they are subject to tidal
intrusion. During sandbar closure, the Butano Marshes become stratified. For example, at station

Pescadero Marsh Restoration Assessment and 46 ESAJ202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

03 (the Boat Launch) (Figures 2 and 4) on November 22,2002, about a month after sandbar
formation, the top foot of the water column was relatively fresh and oxygenated (salinity below
3 ppt, and DO above 2 mg/I), while below about 2 feet quite saline and anoxic (salinity 14-24 ppt,
DO less than .25 mg/I) (Figure 21; see also Figure 22). Stations 0-5 and 0-6 showed similar
saline stratification on this date, with low DO levels throughout the water column. DPR personnel
detected hydrogen sulfide odor at station 03 on November 11,2003, and we detected H2S in the
water column at this station during spot testing on October 2,2003.

Smith and Reis (1997, p. 5) note that tidal intrusion through the enlarged openings in the levees is
rarely enough to introduce salt water into East Butano Marsh, which stayed fresher at station 0-8
than the Middle and North Marsh stations (03 and 06) during sampling in 1995 and 1996.
Swanson (2001, p. 4) notes that much of the summer flow spills out of the aggraded Butano
Creek channel into the lower elevation of East Butano Marsh.

Water temperature was monitored continually at the bottom of the channel at the water level
logger near the footbridge (station WL) from May 22, 2002 through May 29,2003 (Figure 23).
Figure 23 shows the relatively large diurnal temperature range during periods when the mouth of
the creek is open, and the much more restricted range during sandbar formation (September 17 -
December 2, 2002). There was a rapid increase in temperature after sandbar formation, and a
precipitous temperature decline during the storms in early November and December.

Biological indicators

Vegetation Changes
Changes in vegetation sampled by the East Butano Marsh transects (transects Tl and T2; see
Figure 3 and Appendix A) indicate a shift from moderately saline conditions to more
freshwater/brackish conditions between 1985 and 2002. The major trends include a reduction,
then loss, of salt marsh species and a relatively steady increase of brackish and freshwater marsh
species.

The characteristic salt marsh plants, pickleweed and marsh gumplant, present up to and including
the 1990 monitoring, are absent from the 2002 monitoring, as are all other characteristic salt
marsh species. Several brackish marsh species, principally Pacific potentilla, and tule (Scirpus
spp.) have increased substantially over the monitoring period, as have the more characteristically
freshwater marsh species, narrow-leaved and broad-leaved cattails (Typha angustifalia and T
latifoliaj. California blackberry (Rubus ursinus), a species offreshwater wetlands and moist
uplands, has shown a fairly consistent, though generally increasing, presence in the marsh.

As of2002, the marsh area sampled by these transects is for the most part a dense mix of tall
cattails and tules between Pescadero Road and Butano Creek, with patches or strips dominated by
Pacific potentilla and California blackberry nearer to Butano Creek.

Pescadero Marsh Restoration Assessment and 47 ESAI202117


Recol1111endations for Ecosystem Management March 2008
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------------------------------------ Pescadero Marsh Restoration Assessment/202117 -


SOURCE: ESA Figure 21
Station D3 Water Quality
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------------------------------------ Pescadero Marsh Restoration Assessment/202117 -


SOURCE: ESA Figure 22
Station WL Water Quality
2. Review of the 1990 Enhancement Plan

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------------------------------------------- Pescadero Marsh Restoration Assessment / 202117


SOURCE: ESA Figure 23
Station WL Water Temperature, 2002-2003

The amount of open water sampled along the transects had decreased between the 1985 to 1990
monitorings; none was present in the transects in 2002. The areas of North Butano Marsh
sampled by transects T3 and T4 (Figure 3) have differed markedly from each other throughout
the monitoring history. Direction of vegetation change also seem to be divergent, with a
decreased salinity trend suggested by shifts in vegetation for Transect T3 and increased salinity in
the area of Transect T4.

The east portion of North Butano Marsh sampled by Transect T3 was, in the past, a fairly
characteristic pickleweed salt marsh, with pickleweed cover reaching 91 % in 1990. Between
1990 and 2002, a substantial portion of this area shifted to dominance by Pacific potentilla. The
2002 monitoring showed 38% cover of pickle weed and 47% of Pacific potentilla (Pacific
potentilla was present in only one other monitoring- 1985). This increased presence of Pacific
potentilla is mediated by various factors, probably including reduced salinity.

Although only sparsely found in this transect (6% cover in 2002), rabbitsfoot grass (Polypogon
monospeliensis) is present in relatively dense patches in this marsh area. It was not recorded in

PescaderoMarshRestorationAssessmentand 50 ESA/202117
Recommendations
for EcosystemManagement March2008
2. Review of the 1990 Enhancement Plan

the previous monitorings of this transect (or included in earlier plant lists for the Marsh) and can
be considered an additional indication of reduced salinity.

Trends in vegetation change in the more westerly Transect T4 conversely appear to indicate
increased salinity. Cover of characteristic salt marsh species, primarily pickleweed, reached 30%
in 2002, having ranged from 0-8% in past surveys. Cover of the bull tule (brackish species)
decreased from 38% to 26% between 1990 and 2002. Cattails (freshwater species), which reached
a high of22% cover in 1987 were not present in 2002.

Habitat for Species of Concern

California Red-Legged Frog


Smith and Reis (1997) found few California red-legged frog eggs, larvae, juveniles, or adults in
North Butano Marsh in 1996, but found moderate abundance of juveniles and adults in the
Middle and East Butano Marshes. Adult bullfrogs, which prey on California red-legged frogs,
were also present in East Butano Marsh.

Salinity in portions of the Butano Marshes, particularly East Butano Marsh, may be sufficiently
low during the California red-legged frog breeding and rearing seasons (approximately March
through August) to enable reproduction. Because bullfrog larvae do not transform until their
second year, and because they do not tolerate even mildly brackish water, it is unlikely that they
breed successfully in the Butano marshes, which dry down or become salty in most years. Smith
and Reis (1997), however, note the presence of adult bullfrogs in Butano Creek, apparently
having moved down from their more reliable breeding habitat in farm ponds upstream. They
observed that bullfrogs seemed to move downstream and into the marshes, and they were found
in the same locations in East Butano Marsh as California red-legged frog adults and juveniles.
Jennings and Hayes (1990) do not note observation of bullfrogs in the Butano Marshes during
their 1989 surveys.

San Francisco Garter Snake


An assumption was made in the 1990 Enhancement Plan (Williams, 1990) that the Butano left
bank levee and cross-marsh levees provided extensive basking habitat for the San Francisco
garter snake. The Preferred Alternative for the Butano Marshes, as described above, involved
only partial removal of the levees, in order to maintain basking habitat, as well as pedestrian
access to the interior of the Marsh.

By the time of our fieldwork in 2002 and 2003, however, the levees had developed a dense
vegetative cover, potentially reducing their value as basking habitat (though relatively open
patches remained on some parts of the levees). The lack of pedestrian access to some levee
segments restricts the ability ofDPR staff to manage levee vegetation and maintain open basking
habitat. Smith and Reis (1997) report sightings of San Francisco garter snakes at the boundary of
Middle and East Butano marshes, in an area of relative abundance of California red-legged frogs,
in 1996.

Pescadero Marsh Restotation Assessment and 51 ESA/202117


Recommendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

Steel head
As noted previously, Smith (1987, p. 19), observed steelhead using the deeper channels of Butano
Marsh (presumably North Butano Marsh) to feed among the dense pondweed that grew there
during the summer. It is likely that this still occurs.

The presence of hydrogen sulfide at station D3 and of an anoxic layer at station WL indicate that
the channels of the Butano Marshes may be a major area of hydrogen sulfide production. There is
a far greater area of soft mud-bottom, artificial channels in the Butano Marshes than in any other
area of the Marsh. Several dead steelhead smolts were observed along the margins of the main
channel of lower Butano Creek after the sandbar breached in 2001, and several hundred fish were
observed in this area after the sandbar breach in 2003. The Butano Marshes may be a major
source of hydrogen sulfide or anoxic water circulating in the marsh at the breac hing of the
sandbar.

7. Discussion
The implementation of Part 1 of the Butano Marshes Preferred Alternative succeeded in
increasing conveyance of freshwater from Butano Creek into the marshes, as well as increasing
tidal intrusion into the reconnected slough channels and ditches. One consequence of this, which
may not have been intended or foreseen, has been the change in vegetation in East and Middle
Butano Marsh, which are now nearly pure stands oftule, Pacific potentilla, and cattail; and
increasing prevalence of salt marsh vegetation in portions of North Butano Marsh. Leaving
portions of the levees in place succeeded for a short time in the objectives of increasing San
Francisco garter snake basking habitat and allowing pedestrian access into the Marsh. However,
the uncontrolled growth of scrub vegetation on the levees, and the removal of most of the
footbridges and walkways after they were damaged or displaced by high water, have
compromised both of these functions (to the degree that openness defines "basking habitat").

The documented presence of hydrogen sulfide in the water column at station D3 (the Boat
Launch) in the fall of 2003, and the observation by local anglers of tea-colored water flowing out
of the Butano Marshes after the opening of the sandbar that year, both suggest that water quality
conditions in the Butano Marshes could be contributing to fish die-offs. The reconnection of
Butano Creek with the old slough channels, which themselves have been extensively modified,
and the borrow ditch running along the left bank levee have increased circulation between the
Butano Marshes and Butano Creek, beyond what occurred prior to major changes in the Marsh.

8. Recommendations
Desired Conditions
The Butano Marshes should be managed with the goal of maintaining a natural diversity of fresh,
brackish, and salt marshes, and the restoration of floodplain connectivity with Butano Creek, on
the basis that this appears to be the pre-disturbance condition of this portion of the Marsh.

Pescadero Marsh Restoration Assessment and 52 ESA/202117


Reconmendations for Ecosystem Management March 2008
2. Review of the 1990 Enhancement Plan

Recommendations for Further Study and Actions


The following preliminary recommendations would require further analysis both to determine
their ability to meet long-term Marsh management goals, and to understand fully their benefits
and potential adverse impacts.

a. Consider removing the remaining left bank levee between the Pescadero Road bridge and the
Triple Junction, to increase flood conveyance capacity into and through the Butano Marshes.
As suggested by Swanson (200 I), if combined with reconfiguration of the bridge, this would
likely result in a shifting of Butano Creek into the marshes and the re-establishment of a
meandering stream. This would also result in the establishment of a new riparian corridor,
and the creation of backwater areas. If the new channel scours sufficiently (Swanson notes
that reconfiguration of the bridge will be necessary to enable receding floodwaters to scour a
new channel through the marshes), it will enable tidal intrusion during low flow periods into
East and Middle Butano Marsh. The result should be a diversification of habitat types,
including brackish, freshwater, and salt marshes, as well as riparian forest. The old channel of
Butano Creek will likely become a freshwater marsh or back channel.

b. Determine the importance of open areas on the levees for San Francisco garter snake basking
habitat. If lack of such habitat limits the snake population, manage the vegetation on the
remaining levees to maintain open areas, or create new habitat elsewhere. If basking habitat is
not a limiting factor or unimportant in this area, remove the levees to restore the natural
appearance and overbank flood conveyance ofButano Creek.

c. Investigate the extent of hydrogen sulfide formation during sandbar formation, and determine
where it occurs. Depending on the location of the hydrogen sulfide, consider actions to fill or
isolate these areas to prevent free flow of bottom waters into the rest of the lagoon system. If
hydrogen sulfide primarily occurs in the large backwater channel that drains beneath the
footbridge, investigate whether a low weir placed in the artificial channel upstream ofthe
footbridge could prevent laminar flow of bottom waters and reduce disturbance of bottom
sediments during sandbar breaching.

9. Monitoring and Adaptive Management Program for


Butano Marshes
IfButano Creek establishes a new channel through the Butano Marshes, major changes can be
expected in this area of the Marsh. Any filling of existing ditches and artificial channels will also
have an effect on marsh hydrology, which should be monitored. Maintenance of mildly brackish
conditions and seasonal drying of the marshes are desirable, as this should prevent the successful
reproduction of bullfrogs.

a. Conduct surveys for bullfrog presence in the Butano Marshes annually. This may be
accomplished with monitoring for bullfrog calls in the evening in the late spring and early
summer. Monitoring may be done at the footbridge, at station D3, and at pull-outs along
Pescadero Road.

Pescadero Marsh Restoration Assessment and 53 ESA1202117


Recorrmendations for Ecosystem Managerrent March 2008
2. Review of the 1990 Enhancement Plan

b. Continue to monitor for anoxic conditions and H2S formation and circulation. Water quality
should be monitored during lagoon formation and closed sandbar conditions. Efforts should
also be made to observe conditions and sample water quality during sandbar breaches.

c. Conduct surveys at established vegetation transects every 2-3 years.

C. Delta Marshes
The areas on the right bank ofButano Creek, from the agricultural lands west of Water Lane all
the way down to the confluence with Pescadero Creek at Grassy Point, are collectively known as
the Delta Marshes. An artificial channel that runs from the big northward bend in Butano Creek
to the base of Round Hill separates Delta Marsh from East Delta Marsh. The two areas have
experienced widely divergent histories over the past half century: East Delta Marsh was diked,
drained, and used for agriculture, then later restored; while most of Delta Marsh was never diked
and has been relatively undisturbed.

1. Pre-Disturbance Configuration of The Delta Marshes


The 1854 U.S. Coast Survey map of Pescadero Marsh (Figure 6) shows wetland throughout the
same area currently occupied by the Delta Marshes, except that the eastern-most lobe of wetland
depicted on the map is now agricultural land. The map shows numerous slough channels and
ponds throughout the Delta Marshes.

Curry et al (1985, p. 100) note that, prior to construction of a levee and modification of the
channel at the 90 degree bend in Pescadero Creek (which probably occurred prior to 1928),
floodwaters would overtop the left bank of the creek and flow through East Delta Marsh into
Butano Creek at about the apex of the big bend. They state (ibid, p. 102) that the lower course of
Butano Creek is in fact an old channel of Pescadero Creek, and that the prominent slough channel
that can be seen in the 1854 map and early airphotos is a former channel of Butano Creek.

2. Historic Changes to the Delta Marshes


In the 1928 airphoto (Figure 7), the Delta Marshes are essentially unchanged from the 1854
configuration, except that farmland is beginning to encroach from the East. Viollis (1979, p. 128)
notes that in the 1920s, the southeastern corner ofthe marsh, presumably part of East Delta
Marsh, was used as a baseball field and racetrack. Still, it appears that in 1928, there had been no
levee construction or draining of the Delta Marshes.

By 1941, major changes had occurred. The drainage ditch that divides the two marshes can be
seen on the 1941 airphoto (Figure 8), along with the associated levee. Presumably the tide gate
that was installed at the northeast end ofthe ditch (the Phipps Tide Gate) was also in place at this
time, to enable draining of the leveed area after floods. The right bank ofButano Creek, along the
margin of East Delta Marsh, was already leveed. While slough channels are still visible in East
Delta Marsh in 1941, the area was drying out, and there may already have been some extension of

Pescadero Marsh Restoration Assessment and 54 ESA/202117


Recorrmendations for Ecosystem Management Mard12008

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