Ecological Modelling 221 (2010) 11941208

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Ecological Modelling
journal homepage: www.elsevier.com/locate/ecolmodel

Assesment of the response of a shallow macrotidal estuary to changes in

hydrological and wastewater inputs through numerical modelling
Andrs Garca a, , Jos A. Juanes a,1 , Csar lvarez a,1 , Jos A. Revilla a,1 , Ral Medina b,2
a
b

Submarine Outfall and Environmental Hydraulics Group, Institute of Environmental Hydraulics, University of Cantabria, Avda. de los Castros s/n, 39005 Santander, Spain
Ocean and Coastal Research Group, Institute of Environmental Hydraulics, University of Cantabria, Avda. de los Castros s/n, 39005 Santander, Spain

a r t i c l e

i n f o

Article history:
Received 16 June 2009
Received in revised form
20 November 2009
Accepted 31 December 2009
Available online 4 February 2010
Keywords:
Eutrophication
Shallow estuary
Modelling
Phytoplankton
Wastewater discharge
Urdaibai

a b s t r a c t
The aim of this study was to investigate the response to short-term changes in river freshwater discharges
and in nutrients loadings (mainly from the treatment of urban wastewater), of the shallow macrotidal
Urdaibai estuary (north of Spain), by using numerical tools. A two-dimensional hydrodynamic model
and a water quality model were applied to the estuary, in order to better use it as a prediction tool in
the study of the effects of variations in hydrodynamic conditions and in waste water inputs. The model
was calibrated and veried using data measured under different hydrological conditions (spring and
summer). A model calibration was carried out with eld data measured during the summer, while the
model validation was conducted for spring conditions. The calibration process allowed the model parameter denition, while the model validation permitted the verication of the calibrated parameters under
different environmental conditions. The model results were in reasonable agreement with eld measurements, in both the calibration and the validation phases. The model showed a signicant decrease
in phytoplankton concentration with river input increase. A study on the effects of nutrient input reduction from the Gernika Waste Water Treatment Plant (WWTP) was conducted. It showed a decrease in
phytoplankton concentration with decreasing levels of nutrient discharge. This reduction was more pronounced in conjunction with the highest river discharge. In that case, a 50% decrease for the elimination
of the WWTP discharge was observed.
2010 Elsevier B.V. All rights reserved.

1. Introduction
Estuaries receive inorganic nutrients and organic matter from
the land and represent important systems where terrestrial nutrients and organic matter are processed before entering the ocean
(Ortega et al., 2005). As a result, the ecology and biodiversity of
estuarine waters in many parts of the world are under the threat of
increasing anthropogenic nutrient inputs (Nixon, 1995).
Phytoplankton growth is limited by several environmental factors, including light, temperature and nutrients. Among these
factors, only nutrients can be controlled; hence, they have been the
focus of most efforts to control algal blooms responsible of water
quality deterioration (Na and Park, 2006). Knowledge of the nutrient assimilation capacity of estuarine ecosystems is essential for
water quality management and rehabilitation. The main adverse

Corresponding author. Tel.: +34 942201704; fax: +34 942201714.

E-mail addresses: garciagan@unican.es (A. Garca), juanesj@unican.es
(J.A. Juanes), alvarezc@unican.es (C. lvarez), revillaj@unican.es (J.A. Revilla),
medinar@unican.es (R. Medina).
1
Tel.: +34 942201704.
2
Tel.: +34 942201810.
0304-3800/$ see front matter 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.ecolmodel.2009.12.027

effects of uncontrolled eutrophication are depression of oxygen levels and the massive occurrence of harmful algal species. All this has
negative effects on water quality and food webs. Thus, management of aquatic ecosystems has traditionally focused on reducing
nutrient input.
However, besides nutrient control strategies, hydrological
conditions may have an impact on the response of estuarine ecosystems to eutrophication (Chan et al., 2002). Water mass circulation
in estuaries is predominantly controlled by fresh water discharges,
tidal circulation and atmospheric forces. The time scale of physical
processes ranges from hours to seasons and large spatial gradients
affect the hydrographic conditions and nutrient distribution (Dyer,
1997).
The high number of factors inuencing eutrophication processes
has led to consider the use of complex mathematical tools for
studying and predicting their evolution. Water quality models are
essential tools to evaluate the impact of human activities in estuarine ecosystems.
Shallow estuaries are characterized by the presence of wide tidal
ats which yield a considerable variability in the water domain.
This feature increases the difculty of eutrophication modelling
and restricts the application of many water quality models that
have been successfully validated in environments in which water

A. Garca et al. / Ecological Modelling 221 (2010) 11941208

domain changes have no substantial effects, such as deep estuaries

and bays, coastal areas or enclosed seas.
The objective of this study was to develop a quantitative understanding of the Urdaibai estuary response to hydrological inputs
and wastewater loading. The Urdaibai estuary is a shallow unique
habitat for many species. It receives urban inputs, especially from
the village of Gernika, which cause its environmental degradation
(Cortazar et al., 2008). The estuarine ecosystem is also highly variable. During spring and summer, intense phytoplankton blooms
usually develop in the upper reaches of the estuary (Madariaga,
2002).
Several previous studies have been carried out in order to characterize the short-term variability of phytoplankton in the Urdaibai
estuary from eld observations. However, scarce modelling was
used due to the complex geometry of the estuary and the high
variability of river ow and nutrient uxes.
For this study, we set up and implemented a two-dimensional
water quality model for the estuary. Here, we present the calibration and validation of the model based on data measured at
different meteorological and hydrodynamic conditions. Once calibrated, the model was used to study the effect of variations in
hydrodynamic conditions on estuarine water quality. The model
was also applied to analyse future scenarios of nutrient input reduction by the Gernika WWTP. The results and conclusions of these
studies are described.

2. Study area
The Urdaibai Estuary is a meso-macrotidal temperate estuary
located in the Basque Country (43 22 N, 2 40 W), north of Spain
(Fig. 1). An important geomorphological feature of the estuary is
its shallowness (on average 2.6 m deep in the main channel). It
has a drainage area of 149 km2 , being about 12.5 km long, from
its mouth to the city of Gernika, and with a maximum width of
1.2 km.
The estuary receives inputs from several rivers and it is wellmixed to partially mixed depending on river discharge and tidal
range. The strongest salinity gradient occurs generally within less
than 4 km of the upper estuary, where salinity oscillates between
near zero and more than 30 psu. The estuary passes from a wellmixed state during periods of low river discharge and spring tides,
to partially mixed during neap tides or freshets. Thus, the estuary
is river dominated during freshets but tidally dominated during
summer, when river discharges tend to be low (Ruiz et al., 1994).
Water residence time is less than 1 day on average in the lower
estuary due to the large tidal amplitude. Conversely, in the upper
estuary it experiences drastic changes depending on river ow,
oscillating from 1 day to more than 3 months during prolonged
dry periods (Revilla et al., 2002).
The Oka River basin has a drainage area of 67 km2 , with the
main stream covering a distance of 25 km. The average rainfall is
over 1400 mm per year and the overall runoff coefcient is 0.64.
Other rivers entering the estuary are the Mape and the Golako. The
drainage area of the latter is 34 km2 , while the basin drainage of
the Mape River covers an area of 20 km2 .
The estuary is surrounded by relatively broad tidal ats along
its lower reaches and by salt-marshes in its middle part. These geomorphological features determine the estuarine ecosystem, which
can vary considerably in volume and ushing rates, strongly affecting its biological and chemical properties (Madariaga, 2002).
The catchment area is essentially rural, and industrial activities
are mainly concentrated in the town of Gernika, which with a population of 16255 inhabitants, is located in the upper estuary. As a
consequence, estuarine waters receive the discharge of a domestic sewage treatment plant efuent near Gernika that introduces

1195

a considerable amount of nutrients (mainly ammonia and phosphate) to the estuary, causing eutrophication (Fraile et al., 1992).
3. Model description
The model reproduces estuarine water movements during a
tidal cycle using short time steps from hydrodynamic model results
(velocity components, water surface level) obtained by previously
running a two-dimensional hydrodynamic model. This working
scheme allows a larger time step to be selected in order to model
eutrophication than that used for the velocity eld calculation. But
in the case of shallow estuaries, this methodology has the disadvantage that during hydrodynamic data interpolation inside the
water quality model there is a loss of information about the real
instant in which wetting and drying of the tidal at occur. To avoid
this problem, caused by using hydrodynamic results stored separately in time, a subroutine has been included in the model that
allows water surface level to be computed in the entire estuarine domain from two consecutive water level recordings provided
by the hydrodynamic model (Garca et al., 2002). In this way the
exact instant in which shallow areas get wet or dry is accurately
computed.
3.1. The hydrodynamic model
The hydrodynamic and transport models used in this work
solve the two-dimensional vertically integrated hydrodynamic and
transport equations. The numerical computation is carried out on a
spatial domain that represents the entire estuary through a nitedifference grid. The system of equations is expressed in Cartesian
coordinates (x increasing eastward and y increasing northward)
and following the hydrostatic assumption and Boussinesq approximation.
The hydrodynamic model uses the so-called alternating direction implicit technique (ADI), to integrate the depth-averaged mass
and momentum equations in the spacetime domain, which are
expressed as:
H
(UH)
(VH)
+
+
=0
t
x
y

(1)

(UH)
(U 2 H)
(UVH)

gH 2 0
+
+
= fVH gH

20 x
t
x
y
x
+


1 
xz() xz(h) + He
0

e
+H
y

U
V
+
y
x

2 U
2 U
+
2
x
y2

+ 2H

e U
x x

(2)

(VH)
(UVH)
(V 2 H)

gH 2 0
+
+
= fUH gH

20 y
t
x
y
y
+


1 

yz(h) + He
0 yz()

e
+H
x

U
V
+
y
x

2 V
2 V
+
2
x
y2

+ 2H

e V
y y

(3)

where  is the water level (m), g is the gravitational acceleration

(m s2 ), H = h +  is the total water depth (m), h is the undisturbed
water depth (m), U and V (m s1 ) are the vertical integrated velocities, 0 is the average water density, e is the horizontal eddy
viscosity,  iz() and  iz(h) are the wind and bed stresses and f is
the Coriolis parameter. The bottom shear stress is represented as a

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A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Fig. 1. Study area and location of hydrodynamic and water quality sampling stations.

quadratic function of velocity parameterized in terms of the Chezy

friction coefcient (C):
Ui
1
=g

H iz(h)


HDx

T
x


+


HDy

T
y


(7)

U2 + V 2

(4)

C2H

The Chezy friction term can be expressed as a variable dependent

on depth, using the following formula:
C = Mh1/6

(5)

where M is the inverse of the Manning friction coefcient.

Salinity and temperature variations along the estuary are solved
from the depth-averaged transport equation for these variables:
(UHS)
(VHS)

(HS)
+
+
=
t
x
y
x

(UHT )
(VHT )

(HT )
+
+
=
t
x
y
x

S
HDx
x

+
y

S
HDy
y

(6)

where S is the salinity (psu), T is the water temperature ( C) and

Dx and Dy are the diffusivities in x and y. Density is calculated from
spatially variable salinity and temperature through the expression
suggested by UNESCO (1981).
We chose a time interval of 5 s as time step for the hydrodynamic model in order to assure stable conditions. At open
boundaries we prescribed the water level and freshwater ow,
while at the open sea boundary, we prescribed tidal elevation
from the AndersenGrenoble version 95.1 model (Le Provost,
2001).

A. Garca et al. / Ecological Modelling 221 (2010) 11941208

1197

The penetration of incoming solar radiation is described by the

LambertBeer equation:
Iz = I0 exp(Ke z)

(11)
(ly day1 )

where Iz is the light intensity at depth z

calculated from
light surface intensity (I0 ) and the extinction coefcient (Ke ). Daily
I0 , issued by the National Meteorological Institute from the meteorological station G057 located at Mungia, was used in the model.
The total light attenuation coefcient is determined by the effect of
water and chlorophyll a, and can be expressed for the Urdaibai estuary as a function of suspended organic matter and phytoplankton
biomass as follows:
Ke = 0.36948 + 0.99577

2.7

+ C4

(12)

The light-limitation function of Steele and Baird (Thomann and

Mueller, 1987) is used in the model. Vertically averaged G(I) over a
given water depth is integrated as:
G(I) =

2.718
[exp(1 ) exp(0 )]
Ke H

(13)

where
1 =

I0
exp(Ke H)
Is

(14)

0 =

I0
Is

(15)

Fig. 2. Variables of the water quality model.

3.2. The water quality model

The water quality model solves the system of differential equations that describe the main chemical and biological interactions.
The variables of the model are the following (see Fig. 2): ammonia (C1 ), nitrate (C2 ), phosphate (C3 ), phytoplankton biomass (C4 ),
dissolved BOD (C5 ), suspended BOD (C6 ), sediment BOD (C7 ) and
dissolved oxygen (C8 ). The spatial and temporal evolution of these
variables is inuenced by external factors, such as incident solar
radiation, or urban and freshwater discharges.
The water quality model is coupled to the hydrodynamic model
through the transport equation, which integrates the advection and
the diffusion properties of the ow, as well as the basic processes
occurring in the estuary water column:
(UHCi )
(HCi )
(VHCi )

+
+
=
t
x
y
x
+


HDy

Ci
y


HDx

Ci
x

(8)

where Ci is the depth-averaged concentration for water quality (i),

and Ri describes the chemical reaction terms, corresponding to the
interaction equations for state variables.
Algal growth is described by a rst-order kinetic expression
where the rst-order growth rate is dened as the difference
between the growth (Gp ) and the death (Dp ) rates. Phytoplankton
growth (Gp ) is a function of light G(I), temperature G(T) and nutrients G(N), assuming the classical approach that these effects are
multiplicative (Chapra, 1997):
Gp = G(T )G(I)G(N)

(9)

The effect of temperature is expressed as (Thomann and Mueller,

1987):
G(T ) = Gmax GT 20
max

G(N) = min

(C1 + C2 )
C3
,
KmN + (C1 + C2 ) KmP + C3

(16)

The preferential uptake of ammonia as compared to nitrate for

phytoplankton growth kinetics is described as:
PNH3 = C1

(KmN

C2
KmN
+
+ C1 )(KmN + C2 )
(C1 + C2 )(KmN + C2 )

(17)

Phytoplankton mortality is described as the sum of phytoplankton endogenous respiration and zooplankton grazing. The
endogenous respiration rate is expressed as proportional to algal
biomass and the carbon/chlorophyll (CCHL) ratio:


+ Ri H

being Is the saturating light intensity calculated as the weighted

average of light intensity for the previous 3 days (Chau and Jin,
1998).
All of the individual nutrient limitations are computed by a
MichaelisMenten-type expression and the minimum value is chosen for G(N) (Chao et al., 2007):

(10)

were Gmax is the maximum daily growth rate of phytoplankton at

20 C (day1 ) under optimal light and nutrient conditions and Gmax
is the temperature coefcient.

kr = 37.85 CCHL C4

(18)

The CCHL ratio (mg C/mg Chl-a) is considered a variable which

is affected by light, temperature and algae (Cloern et al., 1995):
CCHL = 0.003 + 0.0154exp(0.05 T ) exp(0.059Iav )G(N)

(19)

where Iav is the depth-averaged daily irradiance.

The effect of temperature over endogenous respiration is given
by:
kr (T ) = kr (20 C)rT 20

(20)

where kr is the endogenous respiration rate and  r is a temperature

coefcient.
In the water column, biological oxidation of NH3 to NO3 and
denitrication are all considered a function of temperature and
dissolved oxygen (Chau and Jin, 1998).
The dissolved oxygen concentration at saturation is considered
dependent on both temperature and salinity. To compute the oxygen saturation value we used the following equation (Lopes et al.,
2008):

Cs = 14.652 0.0841S + T 0.0026S 0.41022 + T (S, T )

(21)

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A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Table 1
Water quality model interactions.
Variable

Interaction equation

Ammonia-N

dC1
dt

Nitrate-N

dC2
dt

(T 20)
kn n

Phosphate-P

dC3
dt

(T 20)
Yd2 kd d
C5

Phytoplankton-C

dC4
dt

= G(T )G(I)G(N) (kr r

Dissolved BOD

dC5
dt

= kd d

Suspended BOD

dC6
dt

(T 20)

= Yd kd d

(T 20)

C5 + Ys ks s
C8
(C8 +knit )

(T 20)

Settled BOD

Dissolved oxygen

dC8
dt

= ka a

Vs
H

C6

Vr
H

(T 20)

(T 20)

Yb kb b

(T 20)
Ys2 ks s
C6

+ kdm )

Vph

(T 20)
kdn dn

(T 20)
apc (kr r

kNO
(C8 +kNO )

C8
(C8 +knit )

C1

C2

+ kdm )(1 fop )C4 G(T )G(I)G(N)apc C4

C4

C7

+ kdm )(anc fon + apc fop )C4

(T 20)
kb b
C7

Vph
H

Vs
H

(T 20)

C6 ks s

C4

(Cs C8 ) + G(T )G(I)G(N)

C7 )

(T 20)
Yb2 kb b
C7

(T 20)

+ kdm )anc (1 fon )C4 G(T )G(I)G(N)PNH3 anc C4 kn n

C5

C7 + (kr r

dC7
dt

(T 20)

C7 + (kr r

C1 G(T )G(I)G(N)(1 PNH3 )anc C4

(T 20)

(T 20)

Vr
H

(T 20)

C6 + Yb kb b

 32
12

48
a (1
14 nc

PNH3 ) C4

SOD (T 20)
SOD
H

with
(S, T ) = 0.007991 0.0000374S 0.000077774T

C6

(22)

The re-aeration kinetic constant ka is inuenced by water temperature, ow characteristics (ow velocity and water depth) and
meteorological conditions (wind).
The developed model allows Eq. (8) to be solved by using
an explicit nite-difference scheme based on the split operator
approach, in which advection and diffusion processes are computed independently for each time step. This approach facilitates
the use of different numerical methods for solving each process
(Komatsu et al., 1997). Hence, advective transport is computed
by an upwind scheme while diffusion is described by a centred
scheme. In a further step, changes in water quality concentration
caused by reaction processes are computed. The time step for the
transport model was 30 s, in order to assure stable solutions for
transport equations.
The whole system of equations which describe the interactions
of 8 state variables is presented in Table 1. The symbols along with
the units used for the model are listed in Table 2.
The discharge of the Gernika WWTP is treated as a point-source
input of organic matter and nutrients into the water quality model.
At the discharge cell, a mass balance assuming complete mixing is
made, due to its small water depth.
4. Model calibration
4.1. Field data
A model calibration may be dened as an operation by which
specic values, distributions, or a range of variations are given to
the oating free model parameters, so that the model results t
optimally to a set of eld observations (Lopes et al., 2008). To calibrate the model, both hydrodynamic and water quality data were
needed.
The hydrodynamic model was calibrated and validated with
data measured between January 1998 and February 1998 at six
stations distributed along the estuary. The collected data included
surface elevation, velocities and freshwater inputs from the Oka
and Mape rivers. The location of the sampling stations is shown in
Fig. 1. Two tide gauge stations were located at the middle part of the
estuary (Murueta shipyards) and at the inner part (near the Gernika
WWTP), respectively, during a time period of 15 days. A tidal distortion is observed as the tide moves landwards. This distortion is
more pronounced during spring tides at low tide.
Velocity measurements were carried out at four different locations (stations H1, H2, H5 and H7) distributed along the estuary
during neap and spring tides. Maximum velocities were registered

(T 20)
32
k 
C4
12 r r

(T 20)
64
k 
14 n n

C8
(C8 +kn )

(T 20)

C1 (Yd kd d

(T 20)

C5 + Ys ks s

C6 +

during spring tides near the mouth of the estuary with values
over 1 m s1 . In the upper estuary maximum velocities were about
0.8 m s1 . The velocity eld during spring tides was more than twice
the magnitude found during neap tides.
Time series of water quality variables were measured for a
4-day period in May and July 1999, at four locations in the estuary (stations WQ1, WQ3, WQ5 and WQ7), which are indicated in
Fig. 1. Vertical proles of salinity, temperature, dissolved oxygen
and chlorophyll a were taken. The sampling carried out in May was
intended to evaluate the estuary recovery after a period of heavy
rain. That of July, in contrast, was conducted during a relatively dry
period in order to see the daily changes in water quality associated
with changes in radiation.
In May, salinity remained low and constant at the uppermost
site during the study period. In contrast, station WQ5 experienced strong changes in water salinity, which varied in the surface
from 1.1 psu, on the rst day, to 12.5 psu on the last one. Temperature experienced drastic changes along the estuary, mainly at
station WQ5 which ranged from 16 to 21 C. Oxygen concentrations
remained near saturation level during the sampling period. Temperature experienced a signicant increase at the inner stations,
while it remained constant in the sea area. Chlorophyll a values
were low, both in the river and at the upper estuary. The average
Oka River discharge at the Muxika gauging station in this sampling
period was less than 0.5 m3 s1 , and the tidal range varied between
2.0 and 2.7 m.
During the summer the main physical feature was the decrease
in the oxygen concentration from the mouth towards the upper
estuary. Salinity and temperature remained rather constant. In
the upper estuary, the water column stratication caused by low
river discharges enhanced phytoplankton growth and plankton
metabolism, leading to anoxic conditions for most of the water column. The concentration of chlorophyll a was typical of the summer,
with peaks at station WQ8, and the minimum values in the sea area.
At station WQ1 values lower than 2 g l1 were observed while
at station WQ8, the daily changes in the concentration of chlorophyll, which ranged between 14.8 and 50.2 g l1 , were due to the
effect of solar radiation. The average Oka River discharge during this
period was about 0.13 m3 s1 and the tidal range varied between
1.7 and 2.0 m.
The spatio-temporal variability in the estuary hydrographic
properties during the two surveys is summarized in Table 3. Table 4
shows the nutrient concentrations measured at the mouth of the
main rivers owing into the estuary.
Benthic uxes of dissolved oxygen were derived from data
collected in ve sampling stations along the estuary by Ortega
et al. (2005). The sediment oxygen demand (SOD) varied from
1.5 gO2 m2 day1 at the mouth of the estuary to 8.4 gO2 m2 day1

A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Fig. 3. Sea surface elevation from model results (continuous line) and from the tide gauge located at the Murueta shipyards and at the Gernika WWTP.

Fig. 4. Depth-averaged velocities measured (black dots) and modelled (continuous line) during neap tides.

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A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Table 2
Coefcients and constants used in the model.
Parameter

Description

Value

Units

Fr d
kd
ks
kb
d
s
b
Vr
Vs
Yd
Ys
Yb
Yd2
Ys2
Yb2
anc
apc
kn
n
kdn
 dn
knit
kNO
fon
fop
 SOD
Gmax
Gmax
kmN
kmP
kr
r
kdm
Vph
a

Fraction of dissolved BOD

BOD dissolved degradation rate
BOD suspended degradation rate
BOD settled degradation rate
Temperature coefcient for dissolved BOD degradation
Temperature coefcient for suspended BOD degradation
Temperature coefcient for settled BOD degradation
Resuspension rate of particulate BOD
Settling rate of particulate BOD
Yield factor for release of ammonia by ammonication of dissolved BOD
Yield factor for release of ammonia by ammonication of suspended BOD
Yield factor for release of ammonia by ammonication of settled BOD
Yield factor for release of phosphate from dissolved BOD
Yield factor for release of phosphate from suspended BOD
Yield factor for release of phosphate from settled BOD
Nitrogen/carbon ratio
Phosphorus/carbon ratio
Nitrication rate
Temperature coefcient for nitrication
Denitrication rate
Temperature coefcient for denitrication
Half saturation constant of oxygen for nitrication
Half saturation constant for oxygen limitation denitrication
Fraction of dead algae recycled to organic nitrogen
Fraction of dead algae recycled to organic phosphorus
Temperature coefcient for SOD
Maximum specic growth rate of phytoplankton
Temperature coefcient for growth rate of phytoplankton
Half saturation constant for uptake of inorganic nitrogen
Half saturation constant for uptake of inorganic phosphorus
Endogenous respiration rate of phytoplankton
Temperature coefcient for endogenous respiration
Maximum grazing rate by zooplankton
Settling speed of phytoplankton
Temperature coefcient for re-aeration

0.5
0.4
0.4
0.2
1.047
1.047
1.047
0.1
0.2
0.1
0.1
0.1
0.01
0.01
0.01
0.15
0.009
0.05
1.088
0.1
1.05
2.0
0.1
0.5
0.5
1.09
2.0
1.067
0.025
0.001
0.1
1.045
0.1
0.1
1.024

day1
day1
day1

m day1
m day1
g NH3 -N/g BOD
g NH3 -N/g BOD
g NH3 -N/g BOD
g PO4 -P/g BOD
g PO4 -P/g BOD
g PO4 -P/g BOD
mg N/mg C
mg P/mg C
day1

day1

gO2 m3
gO2 m3

day1

mg N l1
mg N l1
day1

day1
m day1

Fig. 5. Depth-averaged velocities measured (black dots) and modelled (continuous line) during spring tides.

A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Fig. 6. Time series of depth-averaged salinity (, measured; , modelled) and temperature (, measured; - - -, modelled) during spring conditions.

Fig. 7. Time series of depth-averaged salinity (, measured; , modelled) and temperature (, measured; - - -, modelled) during summer conditions.

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A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Fig. 8. Depth-averaged dissolved oxygen (, measured; modelled) and phytoplankton-C (, measured; - - -, modelled) during summer conditions.

Fig. 9. Depth-averaged ammonia (, measured; , modelled) and phosphate (, measured; - - -, modelled) during summer conditions.

A. Garca et al. / Ecological Modelling 221 (2010) 11941208

1203

Fig. 10. Depth-averaged dissolved oxygen (, measured; , modelled) and phytoplankton-C (, measured; - - -, modelled) during spring conditions.

at a location near the Gernika WWTP. Different SODs were

considered for the whole estuary taking into account the bed characteristics and the distance to measuring points.
The discharge ow of the Gernika WWTP ranged between 1560
and 6990 m3 day1 with an average value of 3970 m3 day1 , a
mean 5-day BOD of 60.6 mgO2 l1 , and an average concentration
of ammonium higher than 52 mg NH4 + l1 .

ment with measured data but small deviations are observed during
spring tides, mainly at the shipyards of Murueta. However, this
discrepancy which was due to the complexity inherent in the geometric representation of the estuary and the processes of tidal wave
deformation occurring along it, was not signicant.
Modelled time series of velocities occurring along the estuary
for four different locations were compared with measurements
taken during neap tide (Fig. 4) and spring tide (Fig. 5). The computed velocities were generally quite close to the measured values.
The largest differences were observed at stations 1 and 2, which
were located at the upper site of the estuary. Therefore, it can be
concluded that the hydraulic model reproduced water movement
satisfactorily throughout the estuary.
The calibration procedure for the dispersion coefcient was
performed against the observed salinity for the four stations of
the estuary. Figs. 6 and 7 show the comparison between modelled and observed salinity and temperature. Model salinity results
compared well with eld measurements. A constant dispersion
coefcient of 0.5 m2 s1 was obtained.

4.2. Hydrodynamic model calibration

The model calibration was performed adjusting the bottom
friction coefcient for the entire estuary. In this study the best
adjustment between model results and eld observations was
achieved through bottom roughness parameterized from a variable
Chezy coefcient dependent on water depth. A friction coefcient
M of 45 and an eddy viscosity of 1 m2 s1 were obtained.
Fig. 3 shows the comparison between computed and observed
water surface elevation time series for the two stations located
in the estuary. The model results are in general in good agree-

Table 3
Mean values (STD) of hydrodynamic and water quality parameters at each sampling station.
Survey

Station

Variable
Salinity (psu)

Temperature ( C)

Dissolved oxygen (mg l1 )

Chl-a (g l1 )

PO4 3 (mg l1 )

NH4 + (mg l1 )

Spring

WQ1
WQ3
WQ5
WQ8

34.2
25.3
11.2
0.1

0.7
3.6
5.0
0.0

17.3
18.8
19.0
18.6

0.5
1.0
1.8
1.6

8.1
7.4
7.0
9.1

0.3
0.3
0.5
1.4

1.60
2.44
3.10
0.90

0.77
1.10
2.61
0.30

0.31
0.32
0.24
0.37

0.15
0.11
0.06
0.32

0.06
0.14
0.46
1.36

0.02
0.09
0.14
0.79

Summer

WQ1
WQ3
WQ5
WQ8

34.7
31.4
24.5
14.9

0.2
0.6
1.8
3.3

22.0
22.8
23.3
23.1

0.4
0.4
0.5
0.4

7.2
5.5
3.4
2.6

0.3
0.2
0.6
2.0

1.13
2.57
2.98
29.93

0.33
1.17
0.56
17.50

0.43
0.60
1.20
2.66

0.22
0.12
0.08
0.50

0.05
0.30
1.50
4.92

0.01
0.09
0.19
2.17

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Table 4
Mean values (STD) of water quality parameters in the main rivers.
River

Survey

NO3 (mg l1 )

PO4 3 (mg l1 )

NH4 + (mg l1 )

Chl-a (g l1 )

Oka

Spring
Summer

4.00 0.61
4.86 0.52

0.16 0.02

0.49 0.36

0.84 0.17
0.23 0.10

Golako

Spring
Summer

3.26 0.55
2.16 0.25

0.12 0.05

0.57 0.24

Mape

Spring
Summer

1.57 0.65
1.64 0.37

0.12 0.05

0.50 0.18

4.3. Water quality model calibration and validation

The calibration procedure for the water quality model was performed against data measured along the 4-day survey in July 1999.
Water quality comparisons between eld data and model results
are presented for dissolved oxygen and phytoplankton in Fig. 8.
Fig. 9 shows the comparison of nutrient concentrations measured
and modelled at stations WQ1 to WQ8. The modelled curves show
an important amplitude variation with tidal oscillations that could
not be measured during the eld survey since only one daily sample
was taken at each station. This type of oscillations has been found in
other mesotidal estuaries, such as the Ria de Aveiro lagoon (Lopes
et al., 2008). These uctuations of the amplitude of the concentration made it more difcult to compare model to data. As is shown in
Figs. 8 and 9, the model reproduces the general trend of data. Concerning dissolved oxygen, the mean relative error is lower than 10%
in stations WQ1 to WQ5. The model overestimates phytoplanktonC concentrations for stations WQ3 and WQ5 and underestimates
the phytoplankton-C concentrations for stations WQ1 and WQ8.
The mean relative error is of the order of 20%. In the case of nutri-

ents, the model reproduces the order of magnitude of data, even

though the estimated relative error is of the order or greater than
20%. The calibrated parameter values are presented in Table 2.
Thus, the model could be used as a predictive tool for computing algal growth dynamics and other water quality processes
affecting dissolved oxygen concentrations in shallow water bodies.
Nevertheless, we developed a validation process using the parameters obtained considering the data acquired during May 1999. This
process focused on verifying the model applicability to different
environmental conditions. The comparison between computed and
observed dissolved oxygen and phytoplankton levels is presented
in Fig. 10. Fig. 11 shows the same comparison but for nutrient levels. In these gures it can be observed that the model reproduces
the general trend of observed values and the order of magnitude of
data. The mean relative error is lower than 10% for dissolved oxygen
and phosphate concentrations. Concerning phytoplankton-C and
ammonia concentrations, the mean relative error is of the order or
greater than 20%. The model underestimates the phytoplankton-C
concentration for station WQ1 and overestimates the phytoplankton levels in the innermost stations.

Fig. 11. Depth-averaged ammonia (, measured; , modelled) and phosphate (, measured; - - -, modelled) during spring conditions.

A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Fig. 12. Model results at the Gernika WWTP discharge.

Fig. 13. Time series showing the effect of the hydrodynamic input variability on depth-averaged phytoplankton levels in spring time.

1205

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A. Garca et al. / Ecological Modelling 221 (2010) 11941208

Fig. 14. Time series showing the effect of the hydrodynamic input variability on depth-averaged phytoplankton levels in summer time.

The model results for both periods at the Gernika WWTP discharge are presented in Fig. 12. High nutrient levels as well as
low dissolved oxygen concentrations in summer conditions were
obtained as a consequence of urban waste water inputs.

5. Modelling of the estuary response to environmental

changes
Previous studies carried out in the Urdaibai estuarine ecosystem
(Madariaga and Orive, 1989) showed that phytoplankton biomass
and production in the upper estuary was low during seasonal periods of high river ow and short residence time, but highly increased

during the summer season, when lower river ow and higher residence time occurred.
As has been mentioned before, two eld surveys were carried
out during the year 1999 considering different environmental conditions. The rst one was conducted at the end of May, trying to
represent spring conditions after an increase in freshwater discharges. The second one was carried out at the end of July, under
summer conditions. The comparison between the two periods
shows that the inner zone of the estuary had a higher concentration of oxygen when salinity was very low, whereas when salinity
increased the oxygen concentration decreased. In the same way,
station 5, also in the Gernika channel, only went into hypoxic
conditions when salinity increased. The measured data reected

Fig. 15. Comparison of mean phytoplankton levels at stations WQ3, WQ5 and WQ8 for several pollutant loads of the Gernika WWTP discharge.

A. Garca et al. / Ecological Modelling 221 (2010) 11941208

1207

Fig. 16. Comparison between the phytoplankton biomass concentration levels computed in the current situation and in the hypothetical scenario of eliminating the discharge
of the Gernika WWTP during spring conditions (, without WWTP discharge; - - -, current situation).

Fig. 17. Comparison between the phytoplankton biomass concentration levels computed in the current situation and in the hypothetical scenario of eliminating the discharge
of the Gernika WWTP during summer conditions (, without WWTP discharge; - - -, current situation).

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a signicant decrease in the phytoplankton concentration as the

input of fresh water from the river Oka increased, reaching the
minimum level after a maximum peak in river discharge.
To analyse the inuence of the hydrodynamic input variability
on changes in the phytoplankton level, water quality simulations
were extended to a 15-day period. In this way the effect of tidal
variations on phytoplankton dynamics was taken into account.
Figs. 13 and 14 show the phytoplankton concentrations obtained
at stations WQ1, WQ5 and WQ8 for spring and summer conditions,
respectively. These results highlight the inuence that stems from
the periodic oscillation of the astronomical tide, i.e., the concentration levels of phytoplankton are higher during periods coinciding
with neap tides, with a gradual reduction as the tide rises to periods
of spring tides.
The relationship between oxygen concentration and salinity
reects the impact of water residence time on productivity and
water quality in the estuary. Productivity can be estimated from
phytoplankton biomass, which in previous studies has been shown
to be highly correlated with phytoplankton and bacterial production and respiration rates in the community. On the other hand,
oxygen concentration is a good indicator of water quality. The
inverse relationship between productivity and water quality in the
inner estuary makes it necessary to apply mathematical models
to assist in making decisions about river ow management and
reduction of waste water loads.
Several simulations were run considering different lower pollutant load levels for the Gernika WWTP discharge with respect
to the current situation. Also, a scenario of total suppression of
the waste water discharge was analyzed. In such situations, water
quality indicator variables, especially nutrients and phytoplankton
biomass, were simulated. Fig. 15 presents the model results for the
different input levels studied. The curves shown in this gure indicate the mean 15-day phytoplankton-C concentrations obtained at
stations WQ3, WQ5 and WQ8 as a function of the WWTP discharge
level. It can be observed that the reduction in the nutrient input
caused a lower concentration of phytoplankton within the system.
Obviously, the lowest phytoplankton levels were associated to the
zero discharge. This phenomenon was more pronounced for spring
conditions, that corresponded to higher river discharges (see also
Fig. 16), with a decrease of over 50% in the phytoplankton concentration in stations WQ3 and WQ8. In July, this reduction was smaller
(Fig. 17), due to nutrient concentration decrease was partly neutralized by the improvement in the environmental conditions for
the development of phytoplankton, with respect to those of May. A
phytoplankton concentration decrease of around 20% was obtained
for water quality stations WQ3 and WQ8.
6. Conclusions
A two-dimensional mathematical model for computing
eutrophication changes in the shallow macrotidal Urdaibai estuary
(Basque Country), considering the water domain variability related
to wetting and drying phenomena of the shallowest areas, was
developed and applied. The model was calibrated and veried both
with hydrodynamic and water quality data measured in several
eld surveys. Water quality data collected in May characterized
estuarine conditions after a period of strong rainfall, while data
measured in July reected dry weather conditions.

The reduction in the magnitude of the currents within the estuary due to a decrease in river discharges and tidal range led to an
increase in available nutrients and therefore a signicant increase
in phytoplankton biomass, especially in the innermost stations.
This could increase their potential risk of eutrophication.
The results of modelling considering several reduced input levels from the Gernika WWTP, concluded that there was a decrease
in the phytoplankton concentration in the estuary. The maximum
decrease was obtained with the elimination of the WWTP discharge scenario. This reduction was more pronounced in spring,
when the weather and the increased river discharge were more
favourable to this decline. In such conditions a decrease of about
50% in phytoplankton concentrations was predicted. This phenomenon was not so clear under summer conditions.
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