Modelling Water Quantity and Quality Using SWAT

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Modelling water quantity and quality

using SWAT
A case study in the Limpopo River basin, South Africa
Alterra Report 2405

ISSN 1566-7197
More information: www.wageningenUR.nl/en/alterra
E.P. Querner and M. van Zanen
Modelling water quantity and quality using SWAT
This study has been carried out with support from the Dutch Ministry of Economic Affairs and was also supported by the
EAU4FOOD project, EC Priority Area 'Environment (including Climate Change)', contract
number 265471.
Project code [5237655-01] and [5238573-01]

using SWAT
E.P. Querner1 and M. van Zanen2
1
2
Alterra
Van Hall Larenstein, University of Applied Sciences
Alterra Report 2405

Alterra Wageningen UR
Wageningen, 2013
Abstract
E.P. Querner and M. van Zanen, 2013. Modelling water quantity and quality using SWAT; A case study in the Limpopo River basin,
South Africa. Wageningen, Alterra, Alterra Report 2405, 70 pp.; 28 fig.; 9 tab.; 24 ref.
In the EAU4Food project the enormous challenges African agriculture is facing today are addressed: the agricultural productivity
must increase in the coming years. At present the increase in food production cannot keep up with the population growth. In the
coming years irrigation will gain importance, but at the same time the availability of fresh water and the sustainable use of soil
resources is under increasing pressure. Hence, new approaches are required to increase food production in irrigated areas in
Africa, while ensuring healthy and resilient environments. The need to use less water to produce crops requires innovative
approaches. By using models the aim is to analyse feasible measures to improve water efficiency and to reduce negative impacts.
The SWAT model has been applied in the Nsama sub-basin, which is situated within the Letaba basin in South Africa. SWAT is a
conceptual, physically based hydrological model using daily time steps. In SWAT, a basin to be modelled is divided into multiple
sub catchments, which are then further subdivided into Hydrologic Response Units (HRUs) that consist of a homogeneous land use,
management, ground slope, and soil characteristics. Flow generation, sediment yield, and non-point-source loadings from each HRU
in a sub catchment can be simulated. The purpose of this case study is to use the SWAT model to analyse the effects of changes
to the hydrological system. Because of the lack of data, the model could not be calibrated, instead a sensitivity analysis was
carried out. Measured discharges from the Letaba basin were scaled down to the Nsama in order to compare at that level
measured and calculated discharges. As a test case two scenarios were modelled, being a change in land use and the effect of a
DDT application. Based on the experience of this try-out with the SWAT model and the ArcSWAT user interface, the model will be
used further for analysis of agricultural production changes and their effects on water quantity and quality.
Keywords: modelling, scenarios, SWAT model, Nsama river basin, South Africa.
ISSN 1566-7197
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2013
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Alterra Report 2405

Wageningen, January 2013
Contents
Preface
Summary
2
3
Introduction
11
1.1
1.2
11
11
Soil and Water Assessment Tool (SWAT)
13
2.1
16
Geographic information system ArcGIS10
Limpopo basin, South Africa
19
3.1
3.2
3.3
3.4
3.5
19
20
21
22
23
Situation
Description of the Nsama river basin
Soils and relief
Land use
Hydrology
SWAT model building of Nsama sub basin
25
4.1
25
25
26
26
26
26
28
29
29
30
30
4.2
4.3
Aim of the modelling study

Outline of report
ArcSWAT interface to create model input data

4.1.1 Watershed delineation
4.1.2 Land use, soils and HRU units
4.1.3 Assumptions and other input data
Modelling present situation
4.2.1 Results present situation
4.2.2 Results of the sensitivity analysis
Scenario analysis
4.3.1 Description of the scenarios
4.3.2 Results of the scenario with DDT
4.3.3 Land use change scenario
Conclusions and recommendations
31
5.1
5.2
31
31
Conclusions
Recommendations
Literature
33
Appendix 1 Required steps in ArcGIS10 and SWAT
35
Appendix 2 ArcMap and ArcSWAT metadata of Project
45
Appendix 3 Results of the simulations
47
Appendix 4 Files with specific data
53
Appendix 5 Tips and tricks for ArcSWAT
69
Preface
This report has been partially based on a thesis of the second author as a requirement for the University of
Applied Sciences, Van Hall Larenstein.
This case study was carried out as a try-out of the SWAT model using the ArcSWAT version for ArcGIS 10
(beta version of July 2011), Windows7 and SWAT2009. In November 2012 we downloaded the latest release
of SWAT2012 and ArcSWAT, but the new ArcSWAT version gave so much problems that we went back to the
beta version. The SWAT model was used to explore how easy measures which results in an increasing
agricultural production, preferably using less water and less nutrients, could be handled in the model.
We want to thank the SWAT-team in the USA, especially Raghavan Srinivasan and Nancy Sammons. When we
had questions, they responded very quickly. Also we want to thank mr. N. Javanovic of CSIR for information on
the Lethaba basin, South Africa.
Alterra Report 2405
Alterra Report 2405
Summary
Within the European Union project EAU4Food, cooperative research is intended to investigate the increase in
food production in irrigated farming systems in Africa. There are enormous challenges in African agriculture,
as it is facing today because it has to increase agricultural production in order to keep up with the population
growth. Innovations are needed to reduce the water requirements for a crop. In order to test these
innovations, hydrological models will be used in order to estimate the effects of innovations on water quantity
(water use) and water quality (environmental impact).
The aim of this project is to use the SWAT model (Soil and Water Assessment Tool) to explore the suitability of
this tool to analyse innovations in agriculture. The model was developed to predict the impact of land
management practices on water, sediment and agricultural chemical yields in large complex watersheds with
varying soils, land use and management conditions. The SWAT is now a days used all around the world, mostly
with limited data sets.
In South Africa most of the rivers are temporarily. During the short rainy season they carry water, but in the
remaining dry periods the water flow ceases. The lack of enough water during the dry season is a huge
problem, and especially farmers suffer from this water shortage. Such conditions also prevail in the Limpopo
River basin in Southern Africa. The water resources are limited and irrigation is essential for agriculture.
Therefore the conditions in such a basin are suited to test innovations in soil and water management.
For feasible innovations its needed to estimate the changes in water quantity and quality within a river basin. In
this study the focus is on the Letaba basin, being part of the Limpopo River basin, situated in the northern part
of South Africa where we applied the SWAT model. The SWAT model was set up for the Nsama sub basin,
situated in the northern part of the Letaba basin. The simulation period for the simulation of the present
situation was four years, being from 2004-2007. Because of the limited availability of measured data, the
model was not calibrated. A comparison was made of calculated river flows for the Nsama sub basin against
measured river flows for the Letaba basin. The calculated flow for 2007 resemble the measured flow
reasonably well. A sensitivity analysis was carried out on the major input parameters and the results showed
that there are nineteen out of forty-two parameters sensitive. The most sensitive is the initial SCS runoff curve
number for moisture condition (Cn2).
There are two different scenario defined based on the simulation for the present situation. The first scenario
considers the present situation, but as well water quality is considered, being applications of DDT is simulated.
The second scenario considers a change in land use. The wooded grassland (savannah) is changed in cropand grassland. For the pesticide scenario with DDT, it was the question if the pesticide will bind to soil, will it
be leached out of the soil, will it be dissolve in water or will there be plant uptake. The results show that it
binds to the soil particles. So, DDT shall eventually accumulate within the soil and results in a contaminated
soil. Changing the land use did work very well in SWAT. In the sub catchments 1, 2 and 12 the wooded
grassland was changed nearly all in crop- and grassland. Since irrigation of crops in SWAT was not
considered, the effects of the change in land use on river flows was small.
There were some problems while working with the beta version of ArcSWAT (version July 2011 for Windows7
and ArcGIS 10). The strength of the SWAT model is that all physical processes are included in the model for
estimation of water quantity and quality. The drawback of such a complex modelling system makes it highly
data demanding and therefore rather complex. At the same time sufficient new technologies are developed
Alterra Report 2405
and under development to overcome these data shortage problems, like remote sensing techniques, public
domain data sources, etc. Based on the experience of this try-out with the SWAT model and the ArcSWAT user
interface, the model will be used further for analysis of agricultural production changes and their effects on
water quantity and quality.
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Alterra Report 2405
Introduction
Within the European Union project EAU4Food, cooperative research is intended to increase food production in
irrigated farming systems in Africa. There are enormous challenges in African agriculture, as it is facing today,
to increase agricultural productivity in order to keep up with the population growth. In the coming years
irrigation will gain importance, but at the same time the availability of fresh water and the sustainable use of
soil resources is under increasing pressure. Hence, new approaches are required to increase food production
in irrigated areas in Africa, while ensuring healthy and resilient environments. Therefore innovations are needed
to reduce the water requirements for crop production. In order to test these innovations, hydrological models
will be used in order to estimate the effects of innovations on water quantity (water use) and water quality
(environmental impact).
Many previous attempts to improve food production in irrigated areas did not live up to their expectations,
because of limited involvement of stakeholders, ill-understood socio-economic structures and/or monodisciplinary approaches. To overcome these potential pitfalls of successful adoption of innovations, the
EAU4Food project utilizes a true trans-disciplinary approach, which involves the active participation of all
stakeholders (Froebrich et al., 2011).
In South Africa most of the rivers are temporarily. During the short rainy season they carry water, but in the
remaining dry periods the water flow ceases. The lack of enough water during the dry season is a huge
problem, and especially farmers suffer from this water shortage because the crop production is much less
then potential or even crops dye. Such conditions also prevail in the Letaba basin, South Africa. The water
resources are limited and irrigation is essential for agriculture. Therefore the conditions in such a basin are
suited to test innovations in soil and water management.
1.1
Aim of the modelling study
The aim of this project is to use the SWAT model to explore the suitability of such a modelling tool to analyse
innovations in agriculture. For feasible innovations its needed to estimate the changes in water quantity and
quality within a river basin. These analyses are carried out within the EAU4FOOD project which focusses on
agricultural innovations in Africa. In this study the Letaba basin in the northern part of South Africa is used and
to apply the SWAT model.
1.2
Outline of report
In Chapter 2 an outline of the SWAT model is given. Chapter 3 describes the Letaba basin and the selected
Nsama sub-basin for the SWAT model application. Chapter 4 gives the set-up of the SWAT model and some
results are presented. In Chapter 5 the conclusion and recommendations are given.
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Soil and Water Assessment Tool (SWAT)
The Soil and Water Assessment Tool or its acronym SWAT, is a river basin or watershed scale model. The
model was developed by the United States Department of Agriculture - Agricultural Research Service (USDA ARS) in the early 1990ties. The applications of the SWAT model were initially mainly in the United States, but
now a days it is used all around the world, mostly with limited data sets (Arnold et al., 2009).
The SWAT model is developed to predict the impact of land management practices on water, nutrients,
sediments and agricultural yields in large complex watersheds with varying soils, land use and management
conditions over long periods of time. To satisfy this objective, the model is:
Physically based;
It uses readily available input data;
It is computationally efficient;
It enables users to study long term effects.
For detailed information of those characteristics described above, the reader is referred to the manual with the
theoretical description of SWAT (Neitsch et al., 2011). Model requirements as input data and the model
outputs are described by Arnold et al. (2011). Also available is the SWAT Error Checker in which possible
model inputs in a SWAT project are detected. The way this error checker is used in this project is for
summarizing and presenting water balances (see further Paragraph 4.2). Details on the SWAT model can be
found in numerous reports and papers (e.g. Arnold et al., 1998; Neitsch, 2002a; Neitsch, 2002b; Gassman et
al., 2007). Examples of practical application can be found elsewhere (Arnold et al., 2009; Hunink et al., 2011;
Griensven et al., 2012).
SWAT is a distributed rainfall-runoff model and it needs the river basin to be subdivided into smaller discrete
calculation units for which the spatial variation of the major physical properties are limited, and hydrological
processes can be treated as being homogeneous. The total basin behaviour is the result of the discretized
smaller sub-basins. The maps of soil, land cover and surface slope within each sub-basin, are used to define
unique combinations, and each combination will be considered as a homogeneous unit, i.e. Hydrological
Response Unit (HRU). Hence, SWAT subdivides the river basin into units that have similar characteristics in soil,
land cover and surface slope. Such units are located in each of the considered sub-basins. The water balance
components as shown in Figure 2.1 for each HRU is computed on a daily time step. SWAT deals with standard
groundwater processes. Water enters groundwater storage primarily by percolation, although recharge by
seepage from surface water bodies is also included. Water leaves groundwater storage primarily by drainage
into rivers or lakes, but it is also possible for water to move upward from the water table as capillary rise.
Water can also be extracted for other purposes, like agricultural use or human consumption.
After water is infiltrated into the soil, it can basically leave the ground again as lateral flow from the upper soil
layer - which considers a 2D flow domain in the unsaturated zone - or as return flow that leaves the shallow
aquifer and drains into a nearby river (Figure 2.2). The remaining part of the soil moisture can feed into the
deep aquifer, from which it can be pumped back. The total return flow thus consists of surface runoff, lateral
outflow from root zone and aquifer drainage to river.
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Figure 2.1
Main land phase processes as implemented within SWAT (Neitsch et al., 2011).
Figure 2.2
Schematic diagram of the sub-surface water fluxes.
The water balance in SWAT is the driving force behind flow components in the watershed. To accurately
predict the movement of e.g. pesticides, sediments or nutrients, the hydrologic cycle as simulated by the
model must be as accurate as possible resembling the real situation. Simulation of the hydrology of a
watershed can be separated into two major divisions. The first division is the land phase of the hydrologic
cycle, shown in Figure 2.1. The land phase of the hydrologic cycle controls the amount of water, sediment,
nutrient and pesticide loadings to the main channel in each sub basin. The second division is the water or
routing phase of the hydrologic cycle which can be defined as the movement of water, sediments, etc. through
the channel network of the watershed to the outlet.
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Groundwater
The hydrologic cycle simulated in the SWAT model is based on the water balance equation (for a schematic
representation of the groundwater system, see Figure 2.1):
= 0 +
=1
Where: SWt is the soil water content after time step t of day i; SW0 is the initial soil water content on day i; t is
the time; Rday is the amount of precipitation on day i; Qsurf is the amount of surface runoff; Ea is the amount of
evaporation; wseep is the amount of water entering the unsaturated zone from the soil profile; Qgw is the amount
of return flow as drainage to the surface water. All parameters have the unit mm.
Surface water
A river basin is subdivided into sub basins for the flow routing in the river network. There are two type of
channels within a sub-basin: the main channels and tributary channels considering the drainage within a sub
basin. The flows are routed between sub-basins through the main channels. A typical example of such a
network is shown in Figure 2.3.
Open channel flow is defined as channel flow with a free surface, such as flow in a river. SWAT uses Manning's
equation to define the rate and velocity of flow. As water flows downstream, a portion may be lost due to
evaporation and transmission through the bed of the channel. Another potential loss is removal of water from
the channel. Flow may be supplemented by the fall of rain directly on the channel and/or addition of water from
point source discharges. Flow is routed through the channel using a variable storage coefficient method or the
Muskingum routing method (Chow et al., 1988). Further processes in the channel routing are the movement of
sediment, nutrients and pesticides. Reservoirs may be situated within a catchment and can be contributed for
in the river flow. Reservoirs play an important role in e.g. water supply or flood control. SWAT models four
types of water bodies: ponds, wetlands, depressions/potholes, and reservoirs. Ponds, wetlands, and
depressions/potholes are located within a sub basin off the main channel. Water flowing into these water
bodies must originate from the sub basin in which the water body is located. Reservoirs are located on the
main channel network. They receive water from all sub basins upstream of the water body.
Figure 2.3
A river basin is subdivided into sub basins for the flow routing in the river network.
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The water balance equation of a reservoir in SWAT is (for a schematic picture, see Figure 2.4):
V = Vstored + Vflowin Vflowout + Vpcp Vevap Vseep
Where: V is the volume of water in the reservoir at the end of the day; Vstored is the volume of water stored in
the water body at the beginning of the day (m3); Vflowin is the volume of water entering the water body during
that day; Vflowout is the volume of water flowing out during that day; Vpcp is the volume of precipitation falling on
the water body; Vevap is the volume of water removed from the water body by evaporation; Vseep is the volume
of water lost by seepage.
Figure 2.4
Components of a reservoir with flood water detention (Neitsch et al., 2011).
2.1
Geographic information system ArcGIS10
In this project the geographic information system ArcGIS10 is used. The user interface of the SWAT model in
ArcGIS10 is shown in Figure 2.5. The functionality comprises of different items to set up a project; tools to
delineate the modelling area into sub-basins; to create and edit input data and to carry out SWAT simulations.
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Figure 2.5
The user interface of the SWAT model as a toolbar in ArcGIS10.
The key procedures in ArcGIS to set up a SWAT application are:

Load or select the ArcSWAT extension.
Delineate the watershed and define the HRUs (including land use, soil, and slope as a unique HRU).
Edit SWAT databases (Optional).
Define the meteorological data.
Apply the default input files writer.
Edit the default input files (Optional).
Set up (requires specification of simulation period, PET calculation method, etc.) and run SWAT.
Apply the calibration tool (Optional).
Analyse and visualise SWAT output (VizSWAT) (Optional).
For the Nsama sub basin the above outline of steps is further presented in Chapter 4.
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Limpopo basin, South Africa
3.1
Situation
The case study area is in the north of South Africa, within the South African part of the Limpopo River basin.
The Limpopo basin is an international watershed and lies for 45% in South Africa (Figure 3.1). The remaining
55% is divided across Botswana (20%), Mozambique (20%) and Zimbabwe (15%). The Limpopo River basin
exists of twenty-seven major sub basins, these basins are shown in Figure 3.2. The chosen basin Letaba is
also shown in Figure 3.2. (GIZ Transboundary Water Management in SADC, 2011).
The population within the Limpopo basin is fourteen million, distributed across the four countries. On average
50% of those people live in rural areas. This percentage ranges from 31% in Botswana until 66% in Zimbabwe.
In the Limpopo basin there are two capital cities (Gaborone (Botswana) and Pretoria (South Africa)) and some
major urban centres of these countries (for example: Johannesburg in South Africa).
Figure 3.1
The Limpopo River basin situated partly in South Africa, Mozambique, Botswana and Zimbabwe.
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Figure 3.2
The Limpopo basin with the Letaba sub basin (GIZ Transboundary Water Management in SADC, 2011).
3.2
Description of the Nsama river basin
Figure 3.3 shows in more detail the Letaba basin. There were three requirements for defining the case study
area, being: 1) the area had to be a sub basin of the Letaba; 2) the area should be nearby the city Giyani and
the area had to be approx. 500 km2 and had to be subdivided into approx. 10 sub-catchments. Using these
criteria led to the selection of the river basin Nsama as case study area. The sub-basin is 772 km2 large and
was subdivided into twelve sub catchments. The Nsama river is situated in the north of the Letaba basin and
has a reservoir in it, as shown in Figure 3.3.
Figure 3.3
The Letaba basin with the Nsama river (circled) (GIZ Transboundary Water Management in SADC, 2011).
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3.3
Soils and relief
In the Nsama sub basin there are five different soil types known, as shown in Figure 3.4. There are two soils
types present which are dominant and three other soils having only small areas. The elevation of the basin
ranges from 360 to 810 m+MSL. The upper part of the Letaba basin (Figure 3.3) is considered the Highveld,
whereas the Nsama river lies in the Lowveld. In Figure 3.5 the ground level elevation is shown and in Figure
3.6 the surface slope derived from the elevation map. The slopes are in percentages and the green colours
represents the 0 to 4% slope (0 to 2% is dark green and 2 to 4% is light green). The red areas represent a
slope percentage of more than 8%.
Soil (South African code) % of model area

ZA93
25.1
ZA98
70.5
ZA101
3.0
ZA129
1.0
ZA149
0.3
Figure 3.4
The soils map of the Nsama river basin.
Elevation (m)
% of model area
300 400
5.8
400 500
65.3
500 600
27.4
600 700
1.4
700 800
0.1
800 900
<0.1
Figure 3.5
The elevation range within the Nsama sub basin.
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Slope (%)
% of model area
02
50.5
24
36.3
46
8.0
68
2.4
>8
2.8
Figure 3.6
The slope of the land surface within the Nsama sub basin.
3.4
Land use
Land use is one of the dominant features characterising the hydrological behaviour of an area. The standard
land cover characteristics included in SWAT are all based on conditions in the USA and are therefore not
necessarily valid for Southern Africa. It was beyond the scope of this study to go into details of these
characteristics and therefore we used the standard SWAT land use classes.
A digital land cover map data was obtained from GLCF (Hansen et al., 1998). In that study land cover features,
such as forests, urban area, croplands and sand dunes, were measured and categorized using satellite
imagery. The data we used had a resolution of 1*1 km.
The most pronounced land use in the Nsama river area is wooded grassland or savannah (light brown in Figure
3.7). The second largest land use is woodland (dark brown). The other land uses: agriculture and pastures are
in a minority (Figure 3.7). In the Nsama river basin there is a major rural population with cattle, goats and
subsistence farming (Water Research Commission, 2001).
Land Use
Woodland
Figure 3.7
The land use map of the Nsama river basin.
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% of model area
5.4
Wooded grassland
90.7
Closed shrub land
1.8
Grassland
1.5
Cropland
0.6
3.5
Hydrology
The Nsama river is a sandy lowveld river and is a seasonal river. The term veld is a generic term used to
define certain wide open rural spaces of Southern Africa. It is used in particular to refer to flatter areas or
districts covered in grass or low scrub. In the dry season, the river flow is likely to cease. The river has deeply
incised river channels and wide sandy river beds (Water Research Commission, 2001). In Figure 3.8 there are
two photographs of the river shown.
In the Nsama sub basin a major dam was built, as shown in Figure 3.9. This dam, (Hudson Ntsanwisi or Nsami)
is built in 1976 and has a storage capacity of 29 million m3. The storage characteristics are shown in
Figure 3.10 and in Table 3.1.
Figure 3.8
The Nsama river, Giyani-Punda Bridge (left) and the river with cattle (right) (Water Research Commission, 2001).
Figure 3.9
The Hudson Ntsanwisi dam (Department of Water Affairs, Republic of South Africa and Google Earth, AfriGIS, 2011).
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Figure 3.10
The storage characteristics of the Hudson Ntsanwisi dam (Department Water Affairs Republic of South Africa, 2012).
Table 3.1
The Hudson Ntsanwisi dam characteristics.
Characteristic description
Value
Source
Surface area of reservoir filled to emergency spillway (ha)

Reservoir volume filled to emergency spillway (104 m3)
Area of reservoir filled to principal spillway (ha)
Reservoir volume filled to principal spillway (104 m3)
412
2900
337
2190
A(*) + 10% of A
GIZ Transboundary Water Management in SADC
A(*) - 10% of A
Dep. of Water Affairs, RSA
(*)
24
A is the surface area of the reservoir measured using Google Earth.
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SWAT model building of Nsama sub

basin
The steps to build a SWAT model application is described in the user manual (Arnold et al., 2011). Before
starting the model setup it is recommended to prepare all input tables, including the meteorological data, and
the required GIS maps. For information about the steps in the model setup for the Nsama sub basin, using
ArcGIS10, the reader is referred to Appendix 1. The meta data of ArcMap10 and ArcSWAT is given in
Appendix 2. In Paragraph 4.1 the model set-up for the present situation is described, in paragraph 4.2 the
results and in paragraph 4.3 the scenario analysis is given.
4.1
ArcSWAT interface to create model input data
4.1.1
Watershed delineation
First step to build a SWAT model is defining the model area and dividing it into sub-catchments. Delineation is
done using ground level data and ArcGIS procedures. For the elevation of the ground level a 95*95 m grid
DEM was used (SRTM, 2012; Far et al., 2007). The Shuttle Radar Topography Mission (SRTM) obtained
elevation data on a near-global scale to generate a high-resolution digital topographic database. SRTM
consisted of a specially modified radar system that flew on board of the Space Shuttle Endeavour during an
11-day mission in February of 2000. We used the HydroSHEDS data (Hydrological data and maps based on
SHuttle Elevation Derivatives at multiple Scales), which provides hydrographical information in a consistent
format for regional applications (USGS, 2012). Stream networks and sub-basins are identified and can be used
for the flow routing thru the streams and rivers.
Figure 4.1
Layout of streams and sub-catchments considered in the Nsama sub basin.
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Within SWAT one can define the minimum area of each sub-catchment. There is no optimal number of subcatchments as it depends on the issues addressed in the modelling and scenario analysis, but for our test
case we sub-divided the basin into twelve sub-basins. For the Hudson Ntsanwisi dam it was needed to consider
the dam as a divide between two catchments. This was carried out manually and further details are given in
Appendix 1 (see step 1c of Table A1.2 and Figure A1.1). The streams, main river and sub-catchments are
shown in Figure 4.1.
4.1.2
Land use, soils and HRU units
The land use is crucial for the hydrological cycle. SWAT includes a detailed crop growth module, but we
considered at present the reference evapotranspiration as input data. The land use map was shown in
Figure 3.7 and in Table A1.2 the steps in ArcGIS are given (step 2a).
Soils are the determining factors for hydrological processes such as: surface runoff, infiltration, percolation,
lateral subsurface flow, plant water availability, etc. Since no detailed soil map was readily accessible for the
Nsama we used the soil map of Africa (SOTER). The soil map was shown in Figure 3.4 and in Table A1.2 the
steps in ArcGIS are given (step 2b).
A specific characteristic of the SWAT model is the subdivision of the study area in so-called Hydrological
Response Units (HRUs). These HRUs form a unique combination of a specific soil type, land cover and surface
slope within a sub-catchment. In the model set-up one can limit the number of HRUs in a sub catchment using a
threshold value based on a minimum area criteria for the land cover, soils and land slope. A smaller threshold
value will result in more HRUs. Given the nature of this case study and the importance of land cover a
threshold value of 20% was used for land cover, 10% for soils and 15% for land slope. Using these threshold
values a total number of 63 HRUs were distinguished in the Nsama sub basin.
4.1.3
Assumptions and other input data
During the model building some assumptions were made. These assumptions are:
Soil classification; the USA classification is used instead of the South African soil classification.
Land use is based also on the USA classification instead of the South African. By comparing both
classifications we selected the classification that suites the South African classification.
Mannings 'n' is set to a default value of 0.14.
Precipitation and reference evapotranspiration obtained from meteorological station: B8E008, located at
the Hudson Ntsanwisi dam.
4.2
4.2.1
Modelling present situation

Results present situation
The SWAT model has been run for four meteorological years (2004 - 2007). The years 2004 and 2007 were
wet (above average), while 2005 was a dry year. We could not carry out a calibration of the model, because
there was not sufficient data available for the Nsama sub basin, it was also beyond the present objective of the
study.
In general, three different types of output are being generated by the SWAT model: stream flow in channels,
detailed soil water balances and spatially distributed output. Output generated by SWAT can be large,
26
Alterra Report 2405
depending on the selected output options. One can select output to be written per day, month or year. Output
files can include results for the entire basin, for each sub-catchment or for each HRU. In addition, stream flow
is provided for each sub-catchment and details on reservoir inflow, outflow and storage are given as well.
Figure 4.2 shows the groundwater system and the average flows of the simulation period. Table 4.1 gives a
differentiation of the average flows per year for the groundwater. The yearly average precipitation is for the
study area 271 mm per year and the actual evapotranspiration 210 mm. The potential evapotranspiration is as
high as 1969 mm. From the SWAT simulation it is clear that actual ET is much lower than potential ET, since
irrigation of the agricultural land use was not considered in the simulations. In Appendix 3 the results per
month of each year are given (Tables A3.2 to A3.5 and Figures A3.1 to A3.4).
In 2004, being a wet year, the precipitation amounts to 373 mm and the evapotranspiration was 287 mm.
So the increase in water in the area is 86 mm. The amount of drainage water into the streams and river is
136 mm, being the sum of the groundwater/return flow, the lateral flow and the surface runoff. Not all the
precipitation evaporates, but there is some water stored, mainly as groundwater. In 2005, being a dry year,
only 133 mm of precipitation occurred and 135 mm was the evapotranspiration. So the change in water within
the area is -2.6 mm. This results in a negligible drainage to the streams or river. So, there isnt any
groundwater stored and no flow occurred in the streams and rivers. There is a big difference between the wet
and the dry year. In the wet year there is enough water left, which can be used for agriculture. In the dry year
there is a shortage of water. This shortage affects all life in the case study area, especially the agriculture.
Figure 4.2
Average annual flows of the groundwater system for the period 2004 2007.
Alterra Report 2405
27
Table 4.1
Annual water balance terms (mm) for the Nsama sub basin as simulated by SWAT.
Parameter
Potential evapotranspiration
Actual evapotranspiration
Precipitation
Groundwater flow
Lateral flow
Percolation
Soil water
Surface runoff
2004
2005
2006
2007
1887.3
287.2
373.0
69.8
12.7
78.6
24.6
53.1
1903.8
135.4
132.8
0.0
3.0
0.0
18.9
0.0
1935.9
187.8
221.5
12.3
8.9
14.3
9.8
19.5
2150.7
230.8
356.0
4.4
12.6
6.0
75.6
40.6
Average
1969.4
210.3
270.8
21.6
9.3
24.7
32.2
28.3
Stream flow
SWAT generates stream flow for each sub-catchment. This data can be plotted using the AVSWAT interface, or
exported and visualized with other software packages. We were only able to compare river flows for the
Nsama sub basin, derived from the river flows measured at the Engelhard Dam, which is the gauge shown in
Figure 3.3 and gives measured flows for the entire Letaba basin. We scaled down the measured flow from the
Letaba basin proportionally to the Nsama catchment. In Figure 4.3 a comparison is made for the year 2007.
The calculated flow resemble the measured flow reasonably well. The measured peak flow in Dec 2007 is not
very well simulated by SWAT. We assume that precipitation was concentrated in other parts of the Letaba
basin and not in the Nsama sub basin.
Figure 4.3
Comparison of calculated flows by SWAT and measured flows for the Nsama sub basin (year 2007).
4.2.2
Results of the sensitivity analysis
The SWAT model is a distributed-model with spatially-variable geo-hydrological conditions and land use. It has
therefore hundreds of parameters. Due to the size of the model and the large number of parameters it is not
feasible to do a calibration, like in the case of the Nsama model. Instead a sensitivity analysis developed by
Van Griensven et al. (2002) and included in SWAT model was conducted. The sensitivity analysis has been
carried out for all parameters which can be selected during the setup of the sensitivity analysis in the ArcGIS
interface. It appeared that there are nineteen of the forty-two examined parameters sensitive. Among the most
28
Alterra Report 2405
sensitive parameters were the runoff Curve Number (CN2), the soil evaporation compensation factor (Esco)
and available water capacity (Sd-Awc) (Table 4.1). A full list is given in Appendix 3, Table A3.1.
Table 4.2
Ranking of the five most sensitive parameters for the Nsama model (1 = most sensitive).
Ranking
Parameter code
Parameter definition
1
2
3
4
5
CN2
Esco
Sol_Awc
Sol_Z
Rchrg_Dp
Initial SCS runoff curve number for moisture condition II

Soil evaporation compensation factor
Available water capacity of soil layer (mm/mm)
Depth to bottom of soil layer (mm)
Deep aquifer percolation fraction
4.3
Scenario analysis
4.3.1
Description of the scenarios
The model as developed for the Nsama sub basin, and described in the previous paragraph, is used as a basis
in a scenario analysis. There were two scenarios defined, these are: a scenario with a DDT application and a
scenario with a change in land use. The model is run for a simulation period of four years, being 2004 - 2007,
for which meteorological data was available.
Scenario DDT
This scenario considers the modelling of water quality. The first idea was to model the amount of chloride in
the (surface) water, but pesticides are easier to model in SWAT. Therefore, a pesticide was chosen to be
modelled. The pesticide chosen is DDT, because it has been used in the fifties and sixties of the last century
all over the world and is not allowed to be used in almost all countries (PAN Pesticides Database, 2012). This
is a result of the negative environmental impact it has (e.g. it causes among others: cancer and eggshell
thinning). One of the countries in which DDT is still legal to be used is South Africa (Joemat - Pettersson,
2010). In South Africa DDT is used to kill the malaria mosquito (National Department of Health, 2009).
Modelling the pesticide DDT:
Amount of pesticide (DDT) applied to HRU; all HRUs with agriculture or pasture land use: 10 kg/ha.
Depth of pesticide (DDT) incorporation in soil; all HRUs with agriculture or pasture land use: set on 1 mm.
Initial amount of pesticide (DDT) in soil; all HRUs; 5 mg/kg soil.
Bulk density of channel bed sediment; assumed is 1.5 g/cm3 sediment.
Scenario land use change
The second scenario considers an increase in agricultural land. This scenario will show the effect of a land use
change on river flows.
Modelling land use change:
Wooded grassland (savannah) is split up into:
- Wooded grassland (10%)
- Cropland (75%)
- Grassland (15%)
ArcSWAT model can only change the land uses, when all the different land uses are all present within a sub
basin. Therefore the land use change was considered in sub basins 1, 2 and 12.
Alterra Report 2405
29
In Paragraph 4.3.2 and 4.3.3 the results of the scenarios are presented.
4.3.2
Results of the scenario with DDT
This scenario is based on the present situation (Paragraph 4.2), so only the results of the DDT modelling is
discussed here. In Table 4.3 the average annual results are given. It is interesting to see as outcome that DDT
binds to the soil particles. DDT wont leach out, there is no plant uptake and a little bit of contaminated water in
the lateral flow. So, DDT will accumulate in the soil and/or at soil particles in the water.
Table 4.3
Average annual pesticide (DDT) data (mg/ha).
Parameter
Average annual (mg/ha)
Applied DDT
Decayed
In surface runoff entering stream (dissolved)
In surface runoff entering stream (sorbed)
Leached out of soil profile
In lateral flow entering stream
Final amount of pesticide in ground
4.3.3
160530
149785
7
1040
0.0
0.6
38793
Land use change scenario
The second scenario considers a change in land use. The change is from wooded grassland (SWRN in SWAT)
to cropland (AGRL in SWAT) and grassland (PAST in SWAT). In SWAT these changes can be done by using the
Land Use Update (LUP) table. This management option changes the area of each HRU, so the LUP output table
provides new fractions of the HRU per sub catchment. Table 4.4 gives the change in land use for the Nsama
sub basin. In the land Use Update module, only changes can be made in sub basins in which all the different
land uses are present. So in this scenario the change in land use could be carried out in sub catchment 1, 2
and 12.
Table 4.4
The change in land use of the Nsama sub basin.
Land use in the Nsama sub basin (%) as derived from the HRU data
Existing
Scenario land use
SWRN*
PAST
AGRL
RNGB
95.7
77.4
1.4
4.6
0.8
15.9
2.1
2.1
*) The Land use codes are: SWRN = Wooded grassland; PAST = Grassland; AGRL = Cropland; RNGB = Range Brush.
The changes in land use looks quite drastic, but since the crops in SWAT are not yet irrigated, the change in
water use by the crops is minimal (see also Table 4.1 actual evapotranspiration) and thus also no great
changes in the river flow took place.
30
Alterra Report 2405
Conclusions and recommendations
5.1
Conclusions
The physically-based model SWAT was used to simulate regional groundwater and surface water flow in a
basins with spatially-variable geo-hydrological conditions and land use. Due to the size of the model and the
large number of parameters, the model could not be fully calibrated.
The aim of the project, was to use the SWAT model in order to examine several scenarios with different
changes to improve crop production. Although this was the original aim, the scenario analysis has progressed
not enough. Progress was hampered by the fact that the SWAT model gave problems. Partly this was caused
by the fact that we used a beta version. On the other hand the complexity of the model resulted in less
progress than expected. It wasnt always clear in which file the required information could be found. Therefore
Appendix 4 is added to this report to lookup information on parameters and contents of files. Appendix 5 gives
some tips and tricks how to use ArcSWAT.
The conclusion of this project is that SWAT (or in this case ArcSWAT) can be used for modelling agricultural
changes and water quantity and quality.
The model developed for the Nsama sub basin could not calibrated and validated, and results should therefore
only be considered as a try-out and demonstration application.
In summary the following conclusions can be drawn from the Nsama case study:
The strength of the SWAT model is that all physical processes are included in the model. All processes of
the hydrological cycle can be evaluated, including crop growth, irrigation, and water quality.
The different options of the tool makes it highly data demanding and therefore rather complex. At the same
time sufficient new technologies are being to overcome these problems in data shortage, such as remote
sensing techniques and much more public domain data becomes available on the internet.
Using SWAT there are many research questions to be address, like: impact and adaptation to climate
change, measures to increase crop production and as well in relation to irrigation management, changes in
land cover and/or crops, etc.
5.2
Recommendations
Based on the experience of this try-out with the SWAT model and the ArcSWAT user interface, the model will
be used further for analysis of agricultural production changes and their effects on water quantity and quality.
Also in combination with the Agricultural Policy Environmental eXtender (APEX) model, which can be linked to
the SWAT model.
SWAT has no possibility to convert a reference evapotranspiration into the potential evapotranspiration of the
different land uses in the model application, based on crop factors, like reported by FAO (Allen et al., 1998).
Once crop factors have been implemented in the model it derives the different potential evapotranspiration for
each land use, the actual evapotranspiration is then calculated, based on soil moisture conditions, which is a
standard procedure in SWAT. Such an approach is quite common in regional models like the SIMGRO or
MOGROW model (Querner, 1997).
Alterra Report 2405
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Alterra Report 2405
Literature
Allen, R.G., L.S. Pereira, D. Raes and M. Smith, 1998. Crop evapotranspiration. Guidelines for computing crop
water requirements. FAO Irrigation Drainage Paper no. 56, FAO, Rome, Italy, 300 pp.
Arnold, J.G., R. Srinivasan, R.S. Muttiah and J.R. Williams, 1998. Large area hydrologic modelling and
assessment part I: model development. Journal of the American Water Resources Association. 34(1): 73-89.
Arnold, J., R. Srinivasan, S. Neitsch, C. George, K.C. Abbaspour, P. Gassman, H.H. Fang, A. van Griensven,
A. Gosain, P. Debels, N.W. Kim, H. Somura, V. Ella, L. Leon, A. Jintrawet, M.R. Reyes and S. Sombatpanit
(eds), 2009. Soil and Water Assessment Tool (SWAT): Global Applications. Special Publication No. 4., World
Association of Soil and Water Conservation, Bangkok. ISBN: 978-974-613-722-5, 415 pp.
Arnold, J.G., J.R. Kiniry, R. Srinivasan, J.R., Williams, E.B. Haney and S.L. Neitsch, 2011. Soil and Water
Assessment Tool Input/Output file documentation version 2009, Texas Water Resources Institute, College
Station, Technical Report no. 365
Chow, V.T., D.R. Maidment and L.W. Mays, 1988. Applied hydrology. McGraw-Hill, Inc., New York, NY.
Department Water Affairs Republic of South Africa, Hudson Ntsanwisi dam information and flow data,
http://www.dwaf.gov.za/hydrology/cgi-bin/his/cgihis.exe/StationInfo?Station= B8R009 (Accessed 17 Apr.
2012).
Froebrich, J. et al., 2011. European Union and African Union cooperative research to increase Food
production in irrigated farming systems in Africa. http://cordis.europa.eu/search/index.cfm?fuseaction=
proj.document&PJ_RCN=12121258 (Accessed 10-12-2012).
Gassman, P.W., M.R. Reyes, C.H. Green and J.G. Arnold, 2007. The Soil and Water Assessment Tool:
Historical Development, Applications, and Future Research Directions. Transactions of the ASABE 50(4): 12111250.
GIZ Transboundary Water Management in SADC, Limpopo River Awareness Kit, www.limpoporak.com,
(Accessed 19 Sept 2011).
Google Earth, AfriGIS, Nsama river area, 2012.
Hansen, M., R. DeFries, J.R.G. Townshend and R. Sohlberg, 1998. UMD Global Land Cover Classification, 1
Kilometer, 1.0, Department of Geography, University of Maryland, College Park, Maryland, 1981-1994.
Hunink, W., P. Terink, H. Droogers, J. Reuter and J. Huting, 2011. Towards a Proof-of-Concept of Green Water
Credits, for the Sebou Basin, Morocco. Wageningen, Future Water, Report FutureWater 99.
Joemat-Pettersson, T., 2010. Pesticide Management Policy for South Africa, Government
Gazette/Staatskoerant, 24 December 2010, No. 33899
Limpoporak, 2012. Website http://www.limpoporak.com/en/default.aspx (Accessed 16 Jan 2012).
Alterra Report 2405
33
Longley, P.A., M.F. Goodchild, D.J. Maguire and D.W. Rhind, 2011. Geographic Information Systems &
Science, John Wiley & sons, Inc., Hoboken, 3rd Edition.

National Department of Health, 2009. National Malaria Programme Performance Review 2009, Directorate:
Malaria and other Vector-Borne Diseases, Pretoria.
Neitsch, S.L., J.G. Arnold, J.R. Kiriny and J.R. Williams, 2011. Soil and Water Assessment Tool Theoretical
Documentation, version 2009, Texas Water Resource Institute, Temple, Technical Report no. 406
PAN Pesticides Database, DDT factsheet, http://www.pesticideinfo.org/Detail_ChemReg.jsp?
Rec_Id=PC33482 (Accessed 15 March 2012).
Querner, E.P., 1997. Description and application of the combined surface and groundwater flow model
MOGROW. J. of Hydrology 192: 158-188.
SRTM, 2012. Website: http://www2.jpl.nasa.gov/srtm (Accessed 20 Jan 2012).
USGS, 2011. Website: http://hydrosheds.cr.usgs.gov (Accessed 20 Jan 2012).
Van Griensven, A., A. Francos and W. Bauwens, 2002. Sensitivity analysis and auto-calibration of an integral
dynamic model for river water quality. Water Sci. Technol, 45(9), 325332.
Van Griensven, A., P. Ndomba, S. Yalew and F. Kilonzo, 2012. Critical review of the application of SWAT in the
upper Nile Basin countries. Hydrol. Earth Syst. Sci. 9, 37613788.
Water Research Commission, 2001. State of Rivers Report (2001) - Letaba and Luvuvhu River Systems,
Loretta Steyn Graphic Design Studio, Pretoria, WRC rapport no.: TT 165/01.
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Alterra Report 2405
Appendix 1 Required steps in ArcGIS10

and SWAT
Table A 1.1
Steps in ArcGIS 10.
Step
number
Operation
Description
Location
New Shapefile
Name: Nsama modelarea

Feature Type: Polygon
Spatial Reference:
Description:
WGS_1984_UTM_Zone_34S
All boxes: Unchecked
Output Shapefile/Features:
D:\61-SWAT\STAGE Alterra\Maps\Shapefiles\Nsama modelarea.shp
Create Features
Construction Tools: Rectangle
Polygon to Raster
Input Features: Nsama modelarea.shp

Value Field: ID
Output Raster Dataset: nsama_adjust
Cell assignment type (optional):
CELL_CENTRE
Priority Field (optional): NONE
Cellsize (optional): 100
With Editor
Input Features:
Output Raster Dataset:
D:\61-SWAT\STAGE Alterra\Maps\Rasters\nsama_adjust
Define Projection
Input Dataset or Feature Class:

sotersaf_newsuid_PAWNLimpopo.shp
Coordinate System:
GCS_WGS_1984
File:
D:\61-SWAT\STAGE Alterra\Maps\Shapefiles\bodemkaart\sotersaf_
newsuid_PAWN-Limpopo.shp
Clip
Input Features: sotersaf_newsuid_

PAWN-Limpopo.shp
Clip Features: Nsama modelarea.shp
Output Feature Class: soil_adjust
XY Tolerance (Optional): Empty
Input Features:
D:\61-SWAT\STAGE Alterra\Maps\Shapefiles\bodemkaart\sotersaf_
newsuid_PAWN-Limpopo.shp
Vector
Clip Features:
Output Feature Class:
D:\61-SWAT\STAGE - Alterra\Maps\SWAT input
maps.gdb\dem\soil_adjust
Alterra Report 2405
35
Table A1.1
(continuation): Steps in ArcGIS 10.
Step
number
Operation
Description
Location
Clip
Input Raster: land_clp_m1.tif

Output Extent (Optional): nsama_adjust
Rectangle:
X Minimum: 1471077.538767;
X Maximum: 1527077.538767;
Y Minimum: 7370140.439858;
Y Maximum: 7415740.439858;
Use Input Features for Clipping Geometry
(Optional): Unchecked
Output Raster Dataset: Landuse
Area_adjust.tif
NoData Value (Optional): Empty
Input Raster:
D:\61-SWAT\STAGE Alterra\Maps\Rasters\Landuse\landuse
tiff\land_clp_m1.tif
Map Algebra expression:

Landuse Area_adjust.tif*1
Output Raster: Landuse Area_adjust good.tif
Expression Raster:
D:\61-SWAT\STAGE Alterra\Maps\Rasters\Landuse Area_adjust.tif
Raster
Raster Calculator
Output Extent:
D:\61-SWAT\STAGE Alterra\Maps\Rasters\nsama_adjust
D:\61-SWAT\STAGE Alterra\Maps\Rasters\Landuse Area_adjust.tif
Output Raster:
D:\61-SWAT\STAGE Alterra\Maps\Rasters\Landuse Area_adjust
good.tif
5
36
Feature to Raster
Input Features: soil_adjust

Value Field: NEWSUID_1
Output Raster Dataset: soils-nsama
Output Cellsize (optional): 100
Alterra Report 2405
Input Features:
D:\61-SWAT\STAGE - Alterra\Maps\SWAT input
maps.gdb\dem\soil_adjust
D:\61-SWAT\STAGE Alterra\Maps\Rasters\soils-nsama
Table A1.2
Steps in ArcSWAT 2009.
Step
1
Step name
Operation
Sub operation
Description
Watershed
Delineation
DEM Setup
DEM file:
Input:
D:\61-SWAT\STAGE
Alterra\Maps\Rasters\Dem\dem_projected
Output: D:\61-SWAT\STAGE - Alterra\Nsama,
South Africa\RasterStore.mdb\SourceDem
DEM Projection DEM properties:

Setup
Z-unit: Meter
Remaining properties:
Default
DEM Setup
Input:
Mask:
D:\61-SWAT\STAGE
Alterra\Maps\Rasters\nsama_adjust
Output: D:\61-SWAT\STAGE - Alterra\Nsama, South
Africa\RasterStore.mdb\Mask
Watershed
Delineation
Watershed
Delineation
Watershed
Delineation
Watershed
Delineation
Watershed
Delineation
BurnIn:
Empty
DEM-Based:
Checked
Flow direction and accumulation: Clicked
Area (782 156391): 3127.81936535154 (Ha)
Number of Cells: 3373
Stream Network:
Clicked
Sub basin Outlet:
Checked
Add point source to

each sub basin:
Checked
Add by table:
Empty
Edit Manually:
Add and Delete outlets: See Figure A1.1

In total: 3 points added and 2 deleted
Watershed
Outlet(s)
Selection and
Definition
Whole Watershed
Outlet(s):
Outlet of the Nsama river selected.

See Figure A1.2
Calculation of
Sub basin
parameters
Calculate sub basin

parameters:
Clicked
Add Reservoir:
Clicked in Lake (Hudson Ntsanwisi dam )
Ending
Watershed
Delineation
Exit
Clicked
Output:
Saved (temporary) ESRI files
Report: D:\61-SWAT\STAGE - Alterra\Nsama, South
Africa\Watershed\text\TopoRep.txt
Stream
Definition
Outlet
and Inlet
Definition
Delineate Watershed: Clicked
Number of Outlets: 12 (later 25)

Number of Basins: 12
Alterra Report 2405
37
Table A1.2
(continuation): Steps in ArcSWAT 2009.
Step
2
Step name
a
Operation
Sub operation
Land Use\ Soils\ Land Use Data Land Use Grid:

Slope Definition
Description
Input:
D:\61-SWAT\STAGE - Alterra\Maps\
Rasters\Landuse Area_adjust good.tif
Africa\Watershed\Grid\landuse1
Choose Grid Field:
Value
(click ok)
SWAT Land Use

Classification Table:
Assumptions made for classification code land use. Although

Ive chosen the codes which look a lot like the original
habitat, its not exactly the same.
Overall table
Value
Original Label
New Label (USA)
Code
Woodland
Range Brush
RNGB
Wooded
Grassland
Southwestern US
(Arid) Range
SWRN
Closed
Shrubland
Range Grasses
RNGE
10
Grassland
Pasture
PAST
11
Cropland
Agricultural Land
Generic
AGRL
Land Use Classification Table

Value
Reclassify:
38
Alterra Report 2405
Area (%)
Land Use SWAT
5.39
RNGB
90.67
SWRN
1.80
RNGE
10
1.48
PAST
11
0.66
AGRL
Clicked
Table A1.2
Step
2
Step name
b
Operation
Land Use\ Soils\ Soil Data

Slope Definition
Sub operation
Description
Soils Grid:
Input:
Choose Grid Field:
Value
D:\61-SWAT\STAGE
Alterra\Maps\Rasters\soils-nsama
Africa\Watershed\Grid\landsoils1
Grid Code Value: NEWSUID_1
(click ok)
Options:
Name
SWAT Soil
Assumptions made for classification code soils. Although Ive

chosen the codes which are sandy soils, but its not the
same soil.
Overall table
Value
Original Label
New Label (USA)
ZA93
Lordstown
ZA98
Enosburg
ZA101
Sunapee
ZA129
Killington
ZA149
Success
Soil Classification Table
Land Use\ Soils\ Slope

Slope Definition
Value
Area (%)
Name
25.15
Lordstown
70.49
Enosburg
3.07
Sunapee
1.00
Killington
0.30
Success
Reclassify:
Clicked
Slope Discretization:
Multiple slope
Watershed Slope Stats:
Min: 0.00 Mean: 2.6
Max: 52.0 Median: .0
Slope Classes:
Number of Slope Classes: 5
SWAT Slope
There were no classes yet. In Figure A1.3 you can see the
histogram used for determine the classes.
Slope Classification Table (Limit in %)
Reclassify:
Value
>Lower Limit
<= Upper Limit
9999
Clicked
Alterra Report 2405
39
Table A1.2
Step
2
Step name
d
Operation
Land Use\ Soils\ Ending Land

Slope Definition Use\
Soils\Slope\
Definition
HRU Definition
HRU
Thresholds
Sub operation
Description
Create Feature
Class:
Checked
Africa\Nsama, South Africa.mdb\FullHRU
Create Overlay
Report:
Checked
Output:
D:\61-SWAT\STAGE - Alterra\Nsama, South
Africa\Watershed\text\LandUseSoilsReport.txt
Overlay:
Clicked
HRU Definition:
Multiple HRUs
Threshold:
Percentage
Land Use Percentage 20 %

(%) over sub basin
area:
HRU Definition
HRU Definition
Soil Class
Percentage (%) over
sub basin area:
10 %
Slope Class
Percentage (%) over
sub basin area:
15 %
Land Use
Refinement
(optional)
Land Use Split:
Not done
Land Use
Exemptions:
AGRL Agricultural Land Generic

Cropland
PAST Pasture Grassland
Ending HRU
Definition
Write HRU Report:
Checked
Output:
D:\61-SWAT\STAGE - Alterra\Nsama, South
Africa\Watershed\text\
HRULandUseSoilsReport.txt
Create HRUs:
Clicked:
63 HRUs were created
Weather Data
Definition
Weather
Load US or Custom Custom database: Checked
Generator Data weather database to Locations table:
continue:
D:\61-SWAT\STAGE - Alterra\Tables Nsama
(input)\Weather Generator Gage Location
Table.dbf
Weather Data
Definition
Rainfall Data
40
Weather Data
Definition
Rain gages:
Checked
Precip Time step:
Daily
Locations Table:

(input)\Precipitation Gage Location Table.dbf
Ending Weather OK:

Data Definition
Alterra Report 2405
Clicked
Table A1.2
Step
Step name
Operation
Sub operation
Description
Write input
tables
Write all
Mannings n
Answer of question: No
In new window: 0.14 (default)
Click: OK
Heat Units
Answer of question: No
In new window: 1800 (default)
Click: OK
Sub basin
Characteristics
RES_ESA: 412.5 (ha)

RES_PSA: 337.5 (ha)
RES_EVOL: 2900 (*10^4 m3)
RES_PVOL: 2190 (*10^4 m3)
RES_VOL: 2190 (*10^4 m3)
Editing input
tables
Reservoirs
Run model
Save scenario/model run
Sensitivity analysis
DDT Modeling
Table A1.3
Steps in ArcSWAT 2009 for DDT modeling.
Step
Step name
Operation
Sub operation
Description
D1
Editing input
tables
Management
(.mgt) table
Operations (tab)
Add operation: Pesticide Application
Soil chemical
(.chm) table
Soil pesticide data
Pest_ID: DDT
PST_Kg: 10
PST_dep: 1 mm
Save edits
Add pesticide: DDT
Solpst: 5 mg/kg
Rest: default
Save edits
General data
(.bsn) table
Reaches
Routing pesticide: DDT

Rest: default
Save edits
Routing (.rte)
table
RTE parameters
CH_Bed_BD: 1.5 grams/cm3

Rest: default
Save edits
D2
Rewrite input tables: .mgt, .chm, .bsn and .rte
D3
Run model
D4
Alterra Report 2405
41
Land use change

Table A1.4
Steps in ArcSWAT 2009 for land use change.
Step
Step name
Operation
Sub operation
Description
L1
Land use
Update
Add land use

update
Land use to update
SWRN
Start date
1 January 2004
(split land use table)

Land use
New Land use
Percent
SWRN
AGRL
75
SWRN
PAST
15
SWRN
SWRN
10
Apply to selected sub 1

basins
2
12
Saving edits
L2
Rewrite .LUP table
L3
Run model
L4
Figures by the required schematisation steps
Figure A1.1
Manually added nodes and the deleted nodes.
42
Alterra Report 2405
Click: OK
Creating: LupInput0.dat (in TxtInOut folder)
Nsama sub basin
Figure A1.2
Selected outlet point.
Figure A1.3
Histogram of Slope for classification.
Alterra Report 2405
43
44
Alterra Report 2405
Appendix 2 ArcMap and ArcSWAT metadata of

Project
SWAT project settings:

Project setup:
Project Directory:
D:\61-SWAT\STAGE - Alterra\Nsama, South Africa
SWAT Project
Database:
Personal Geodatabase
Name (*mdb):
Nsama, South Africa\Nsama, South Africa.mdb
Raster Storage:
Name (*mdb):
RasterStore.mdb
SWAT Parameter
Geodatabase:
Name (*mdb):

(input)\SWAT2009.mdb
Name ArcGIS
Map (*mxd):
Nsama, South Africa.mxd
Settings used in Nsama, South Africa.mxd:

Environments:
Data frame
properties:
Workspace:
Current Workspace:
(File geodatabase) D:\61-SWAT\STAGE - Alterra\Nsama, South

Africa\Workspace.gdb
Scratch Workspace:
(File geodatabase) D:\61-SWAT\STAGE - Alterra\Nsama, South

Africa\Workspace.gdb
Output
coordinates:
Output coordinate
system:
(As specified
below)
General:
Name:
Nsama, South Africa
Description:
An SWAT casestudy of the Nsama sub basin.
Credits:
M. van Zanen, Alterra
Units:
Data frame:
Map:
Meters
Display:
Meters
Simulate layer
transparency in
legends:
Checked
Extent:
Automatic
Clip options:
Clip to shape
Clip grids and
graticules:
Coordinate
system:
Checked
The remaining settings in the Environments and Data frame properties are default.
Alterra Report 2405
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46
Alterra Report 2405
Appendix 3 Results of the simulations
Sensitivity analysis
Table A3.1
Table with the sensitive parameters and their ranking.
Ranking
Parameter code
Parameter definition
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
Cn2
Esco
Sol_Awc
Sol_Z
Rchrg_Dp
Blai
Epco
Slope
Alpha_Bf
Ch_K2
Canmx
Surlag
Gw_Revap
Sol_K
Gw_Delay
Ch_N2
Slsubbsn
Biomix
Nperco
Initial SCS runoff curve number for moisture condition II

Available water capacity of soil layer (mm/mm)
Depth to bottom of soil layer (mm)
Maximum potential leaf area index for land cover/plant
Plant uptake compensation factor
The mean slope within the HRU
Base flow alpha factor
Effective hydraulic conductivity in main channel alluvium (mm/hour)
Maximum canopy storage (mm H2O)
Surface runoff lag time (days)
Groundwater re-evaporation coefficient
Saturated hydraulic conductivity of soil layer (mm/hour)
Groundwater delay (days)
Mannings 'n' value for main channel
Average slope length (m)
Biological mixing efficiency
Nitrogen percolation coefficient
Alterra Report 2405
47
Present Scenario
Table A3.2
Total monthly basin values for 2004 (see also graph A3.1).
Month
28.96
0
0.41
0
209.3
18
72.15
0.05
33.19
0.09
4.06
6.19
156.1
123
138.28
13.16
65.22
21.03
7.47
72.5
108.7
186
139.38
39.96
42.38
27.59
0
0
120.5
0
97
0
42.37
15.68
0
0
118.5
0
54.63
0
20.62
3.68
0
0
101.6
0
34.01
0
11.57
1.13
0
0
139.8
0
22.44
0
Parameter
Evapotranspiration (mm)
Groundwater flow (mm)
Lateral flow (mm)
Percolation (mm)
Potential evapotranspiration (mm)
Precipitation (mm)
Soil water (mm)
Surface runoff (mm)
Month
10
11
12
Average
Parameter
Lateral flow (mm)
Percolation (mm)
Precipitation (mm)
Soil water (mm)
Surface runoff (mm)
Figure A3.1
Total monthly basin values for 2004.
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Alterra Report 2405
2.18
0.41
0
0
153.5
0
20.26
0
0.08
0.15
0
0
174.4
0
20.18
0
11.97
0.06
0.17
0
209.3
13
21.03
0
4.82
0.02
0.04
0
212.7
4
20.18
0
23.9
0.01
0.63
0
182.9
29
24.65
0
23.94
5.82
1.07
6.56
157.28
31.08
55.35
4.43
Table A3.3
Total monthly basin values for 2005 (see also graphs A3.2 and A3.3).
Month
15.04
0
0.48
0
187.9
21
30.13
0
9.24
0
0
0
181.3
0
20.88
0
10.34
0
0
0
160.1
1.8
12.34
0
25.3
0
0.81
0
110.1
36
22.21
0.01
19.9
0
0.02
0
124.8
0
2.31
0
0.89
0
0
0
113.4
0
1.42
0
0.5
0
0
0
135.9
0
0.92
0
Parameter
Lateral flow (mm)
Percolation (mm)
Precipitation (mm)
Soil water (mm)
Surface runoff (mm)
Month
10
11
12
Average
Parameter
Lateral flow (mm)
Percolation (mm)
Precipitation (mm)
Soil water (mm)
Surface runoff (mm)
0.24
0
0
0
134.8
0
0.68
0
0.36
0
0
0
208
0
0.33
0
0.33
0
0
0
217
0
0
0
14.05
0
0.33
0
179.7
16
1.62
0
39.26
0
1.38
0.02
150.8
58
18.93
0.01
11.29
0.00
0.25
0.00
158.65
11.07
9.31
0.00
Figure A3.2
The total monthly basin values for 2005. Because of the value ranges, the potential evapotranspiration is presented separately.
Alterra Report 2405
49
Table A3.4:
Total monthly basin values for 2006 (see also graph A3.4).
Month
59.57
2.39
8.58
14.33
155.5
201
117.93
19.54
15.02
5.27
0
0
154.2
0
102.91
0
16.81
3.4
0
0
101.7
0
86.09
0
33.29
0.77
0
0
107.7
0
52.8
0
27.01
0.29
0
0
141.1
0
25.8
0
11.26
0.11
0
0
119.9
0
14.53
0
4.36
0.04
0
0
130.8
0
10.17
0
Parameter
Lateral flow (mm)
Percolation (mm)
Precipitation (mm)
Soil water (mm)
Surface runoff (mm)
Month
10
11
12
Average
Parameter
Lateral flow (mm)
Percolation (mm)
Precipitation (mm)
Soil water (mm)
Surface runoff (mm)
Figure A3.3
Total monthly basin values for 2006.
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Alterra Report 2405
0.39
0.02
0
0
178.4
0
9.78
0
0.01
0.01
0
0
202.4
0
9.77
0
0
0
0
0
209.7
0
9.77
0
19.95
0
0.37
0
228.1
20.5
9.95
0
0.14
0
0
0
206.4
0
9.81
0
15.65
1.03
0.75
1.19
161.33
18.46
38.28
1.63
Table A3.5
Total monthly basin values for 2007 (see also graphs A3.5 and A3.6).
Month
0
0
0
0
0
9.77
0.04
195.5
0
0
0
0
0
9.77
0
194.5
168
32.64
5.68
0.02
4.91
109.05
24.5
222.1
0
0.17
0.82
1.81
0.28
72.22
36.55
146.8
0
0
0
1.56
0
34.2
38.02
148.4
0
0
0
0.44
0
1.16
33.04
253.6
0
0
0
0.17
0
0.89
0.27
169.2
Parameter
Precipitation (mm)
Surface runoff (mm)
Lateral flow (mm)
Percolation (mm)
Soil water (mm)
Month
10
11
12
Average
Parameter
Precipitation (mm)
Surface runoff (mm)
Lateral flow (mm)
Percolation (mm)
Soil water (mm)
0
0
0
0.06
0
0.81
0.08
178.2
100
6.97
3.11
0.02
0.22
82.81
6.82
177
0
0.15
0.74
0.15
0
56.52
26.29
149.9
0
0
0
0.12
0
48.19
8.33
160.2
88
0.68
2.29
0.11
0.61
75.66
56.92
155.3
29.67
3.38
1.05
0.37
0.50
41.75
19.24
179.23
Figure A3.4
The total monthly basin values for 2007. Because of the range in values, the graph is split up.
Alterra Report 2405
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Alterra Report 2405
Appendix 4 Files with specific data
In this Appendix only the important input and output parameters are given. These parameters are ordered per
subject. Both the subjects and the parameters within the subjects are in alphabetical order. A complete list of
the input parameters is available in the ArcSWAT Interface for SWAT 2009; Users Guide (Winchell et al.,
2010) Appendices 1 and 3 and in the Soil and Water Assessment Tool Input/Output file documentation
(Arnold, J.G. et al., 2011). A complete list for the output parameters is available in the Soil and Water
Assessment Tool Input/Output file documentation (Arnold, J.G. et al., 2011) in Chapter 32.
Input parameters: Data files made by SWAT
Original SWAT file: Tables input (self-made folder outside SWAT Project Folder)\SWAT2009.mdb
(In this case study: Tables Nsama (input)\SWAT2009.mdb)
For Tables A4.1 until A4.12:
Folder within SWAT project: Scenarios\(saved scenario name)\TablesIn
(In this case study: (Nsama, South Africa\)Scenarios\ SWAT default scenario present)\TablesIn)
Database file: (SWAT Project Name).mdb
(In this case study: Nsama, South Africa.mdb)
Basin, HRU, Sub Basin and Watershed

Table A4.1
The basin, HRU, sub basin en watershed input parameters.
Data
Table
Column
Definition
Amount of HRUs in a sub

basin
Area of basin
Area of HRU
Area of sub basin in ha
Area of sub basin in ha
Area of sub basin in
kilometres2
Classes slope map
Sub
HRUTOT
Number of HRUs in sub basin
ArcHydro\Basin
FullHRU
ArcHydro\Watershed
Hrus
Sub
Shape_Area
AREA
Area
ARSUB
SUB_KM
Area of shape (m2)

Area of HRU (m2)
Sub basin area (ha)
Sub basin area (ha)
Sub basin area (km2)
SlopeRemap
(whole table)
Elevation of sub basin

Fraction of sub basin
area covered with
specific HRU
Reach depth in sub basin
Sub
Hru
ELEV
HRU_FR
This table contains the reclassify table

for the multiple slope classes
Elevation of sub basin (m)
Fraction of sub basin area contained in
HRU (km2/km2)
ArcHydro\Watershed
Dep1
Sub basin tributary reach depth (m)
Alterra Report 2405
53
Table A4.1 (continuation): The basin, watershed, sub basin en HRU input parameters
Data
Table
Column
Definition
Reach depth in sub basin

(per HRU)
Reach slope in sub basin
Reach width in sub basin
Slope of sub basin
Summary of HRU
characteristics
FullHRU
MEAN_SLOPE
Sub basin tributary reach depth (m)
ArcHydro\Watershed
ArcHydro\Watershed
ArcHydro\Watershed
FullHRU
Csl
Wid1
Slo1
UNIQUECOMB
Summary of HRU
characteristics
Hrus
UNIQUECOMB
Sub basin tributary reach slope (%)

Sub basin tributary reach width (m)
Sub basin slope (%)
Unique string for the HRU composed of a
concatenation of the land use, soil, and slope
text codes
Unique string for the HRU composed of a
concatenation of the land use, soil, and slope
text codes
Hydrology and Water Quantity

Table A4.2
The hydrology and water quantity input parameters.
Data
Table
Column
Definition
Base flow factor

Deep aquifer percolation
factor
Groundwater delay time
Groundwater height
Lateral flow travel time
Mannings n
Re-evaporation coefficient
Gw
Gw
ALPHA_BF
RCHRG_DP
Base flow alpha factor (days)

Gw
Gw
Hru
Hru
Gw
GW_DELAY
GWHT
LAT_TTIME
OV_N
GW_REVAP
Groundwater delay time (days)

Initial groundwater height (m)
Lateral flow travel time (days)
Mannings n value for overland flow
Groundwater re-evaporation (revap) coefficient
54
Alterra Report 2405
Land Use and Soil

Table A4.3
The land use and soil input parameters
Data
Table
Column
Definition
Exemptions of land use

threshold
LuExempt
(whole table)
Land use types (general)
Crop
(whole table)
Land use types used in

SWAT modeling
Luso
(whole table)
Soil types (general)
Sol
(whole table)
This table contains records of the SWAT land

use classes that have been designated as
being exempt from the area threshold defined
during HRU delineation
This table contains the land use types, with
specifications, for input into SWAT
This table contains records of the SWAT land
use classes that are exempt from or survived
the area thresholds defined during HRU
delineation. The area (m2) covered by a
specific land use within a sub basin is given.
This table contains the soil types, with
Alterra Report 2405
55
Other Important Input Parameters

Table A4.4
Other important input parameters.
Data
Table
Column
Definition
Maximum input variable
Autoinpar
MAX
Minimum input variable
Autoinpar
MIN
Overall SWAT project table
MasterProgress
(whole table)
Parameter level
Autoinpar
TYPE
Which steps are already

taken?
Cio
ICLB
Soil types (general)
Sol
(whole table)
Maximum value allowed for SWAT input

variable
Minimum value allowed for SWAT input
variable
This table contains information about the
SWAT project, including data paths, datasets,
and the steps that have been completed in the
model
Parameter level code
1: basinlevel parameter
2: sub basinlevel parameter
3: HRUlevel parameter
4: croplevel parameter
Automated method flag
0: no automated method performed
1: sensitivity analysis
2: uncertainty analysis/auto calibration
3: sensitivity analysis and uncertainty
analysis/auto calibration
Default at start: flag 0
When method flag is 1, 2 or 3: the filename of
the auto-calibration parameters file is given in
column CALFILE
This table contains the soil types, with
56
Alterra Report 2405
Output
Table A4.5
Input parameters for output.
Data
Table
Column
Definition
Number of years to not

print out
Printing binary output
Cio
NYSKIP
Cio
IA_B
Printing channel velocity

and water depth
Cio
ITEMP
Printing hourly output
Cio
IPHR
Printing management
output
Cio
IMGT
Printing soil storage

values
Cio
ISTO
Printing water quality
Cio
IHUMUS
Routing headwaters
Cio
I_SUBW
Stream flow print out
Cio
ILOG
Time step output
Cio
IPRINT
Number of years to not print out

Default: value 0
Code for binary output of files (.rch, .sub, .hru
files only)
0: do not print binary files
1: print binary files
Code for printing channel velocity and water
depth output files
0: do not print chanvel.out and watrdep.out
1: print chanvel.out and watrdep.out
Code for printing hourly output file (hourq.dat)
0: no print
1: print file
Code for printing output.mgt file
0: do not print output.mgt
1: print output.mgt
Code for printing soil storage values by soil
layer (soilst.out)
0: no print
1: print file
Code for output file for humus
0: do not print watqual.out file
1: print watqual.out file
Code for routing headwaters
0: do not route
1: route
Stream flow print code
0: print stream flow in .rch file
1: print log of stream flow in .rch file
Recommended: code 0
Print code
0: monthly output
1: daily output
2: annually output
Alterra Report 2405
57
Reaches
Table A4.6
The reach input parameters.
Data
Table
Column
Definition
Average depth of main

channel
Average slope of main
channel
Average slope of tributary
channel
Average width of main
channel
Average width of tributary
channel
Channel degradation
Rte
CH_D
Average depth of main channel (m)
Rte
CH_S2
Sub
CH_S1
Rte
CH_W2
Average slope of main channel along the

channel length (m/m)
Average slope of tributary channel along the
channel length (m/m)
Average width of main channel (m)
Sub
CH_W1
Average width of tributary channel (m)
Bsn
IDEG
Channel water routing
Bsn
IRTE
Channel width - depth ratio

Drainage area of reach
Effective hydraulic
conductivity in main
channel
Effective hydraulic
conductivity in tributary
channel
Fraction of transmission
losses from main channel
to deep aquifer
Rte
Archydro\Reach
Rte
CH_WDR
AreaC
CH_K2
Channel degradation code

0: channel dimensions are not updated as a
result of degradation
1: channel dimensions are updated as a
result of degradation
Recommended: code 0
Channel water routing method
0: Variable storage method
1: Muskingum method
Default: method 0
Channel widthdepth ratio
Cumulated drainage area (ha)
Effective hydraulic conductivity in main
channel alluvium (mm/hour)
Sub
CH_K1
Effective hydraulic conductivity in tributary

channel alluvium (mm/hour)
Bsn
TRANSRCH
Length of main channel

Longest tributary channel
length
Mannings 'n' for main
channel
Mannings 'n' for tributary
channel
Reach depth
Rte
Sub
CH_L2
CH_L1
Rte
CH_N2
Fraction of transmission losses from main

channel that enter deep aquifer. The
remainder if the transmission losses enter
bank storage.
Default: value 0.00
Length of main channel (km)
Longest tributary channel length in sub basin
(km)
Mannings n value for main channel
Sub
CH_N1
Mannings n value for tributary channel
Archydro\Reach
Dep2
Stream reach depth (m)
58
Alterra Report 2405
Table A4.6
(continuation): The reach input parameters.
Data
Table
Column
Definition
Reach drains into sub

basin
Reach evaporation factor
ArcHydro\Reach
SubbasinR
Bsn
EVRCH
Reach length
Reach slope
Reach starts in sub basin
ArcHydro\Reach
ArcHydro\Reach
ArcHydro\Reach
Len2
Slo2
Subbasin
Reach width
ArcHydro\Reach
Wid2
The sub basin grid code that the reach

drains to
Reach evaporation adjustment factor.
When no value is entered, the value will set at
1.00
Stream reach length (m)
Stream reach slope (%)
The sub basin grid code that the reach
begins in
Stream reach width (m)
Reservoir
Table A4.7
The reservoir input parameters.
Data
Table
Column
Definition
Area of reservoir filled to

emergency spillway
Area of reservoir filled to
principal spillway
Reservoir volume
Volume of reservoir filled
to emergency spillway
Volume of reservoir filled
to principal spillway
Res
RES_ESA
Res
RES_PSA
Res
Res
RES_VOL
RES_EVOL
Res
RES_PVOL
Reservoir surface area when the reservoir is

filled to the emergency spillway (ha)
Reservoir surface area when the reservoir is
filled to the principal spillway (ha)
Initial reservoir volume (104 m3)
Volume of water stored in reservoir when filled
to the emergency spillway (104 m3)
Volume of water stored in reservoir when filled
to the principal spillway (104 m3)
Simulation
Table A4.8
The simulation input parameters.
Data
Table
Column
Definition
End date of simulation

First simulation year
Number of years
simulated
Start date of simulation
Cio
Cio
Cio
IDAL
IYR
NBYR
Ending Julian day of simulation

Beginning year of simulation
Number of calendar years simulated
Cio
IDAF
Beginning Julian day of simulation
Alterra Report 2405
59
Surface Runoff
Table A4.9
The surface runoff input parameters.
Data
Table
Column
Definition
Bypass flow modeling
Bsn
ICRK
Daily curve number

calculation
Bsn
ICN
Rainfall, runoff and routing

option
Bsn
IEVENT
Surface runoff lag time
Bsn
SURLAG
Crack/bypass flow code

0: dont model crack flow in soil
1: model crack flow in soil
Daily curve number calculation method
0: calculate daily CN value as a function of
soil moisture
1: calculate daily CN value as a function of
plant evaporation
Rainfall/runoff/routing option
0: daily rainfall/curve number runoff/daily
routing
1: daily rainfall/Green & Ampt infiltration/daily
routing
2: sub-hourly rainfall/Green & Ampt
infiltration/daily routing
3: sub-hourly rainfall/Green & Ampt
infiltration/hourly routing
Default: option 0
Surface runoff lag time (days)
Water Balance
Table A4.10
The water balance input parameters.
Data
Table
Column
Definition
Initial soil water storage
Bsn
FFCB
Leaf area index with no

evaporation of water
PET method
Bsn
EVLAI
Bsn
IPET
Plant uptake
compensation factor
Soil evaporation
compensation factor
Bsn
EPCO
Initial soil water storage expressed as a

fraction of field capacity water content
Leaf area index at which no evaporation
occurs from water
PET method code
0: PriestleyTaylor method
1: Penman/Monteith method
2: Hargreaves method
3: Read in potential ET values
When method code is 3: the filename of the
read in file is given in column ETFILE
Plant uptake compensation factor
Bsn
Hru
ESCO
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Water Quality
Table A4.11
The water quality input parameters.
Data
Table
Column
Definition
In-stream water quality

modeling
Bsn
IWQ
Sub basin water quality

modeling
Bsn
ISUBWQ
In-stream water quality code

0: do not model in-stream nutrient and
pesticide transformations
1: model in-stream nutrient and pesticide
transformations
Default: code 0
Sub basin water quality code
0: do not calculate algae/CBOD loading and
set dissolved oxygen to saturated oxygen
concentration
1: calculate algae/CBOD loadings/Dissolved
oxygen using algorithms documented in
SWAT Theoretical document (Neitsch, S.L.
et al, 2011)
Default: code 0
Weather and Climate

Table A4.12
The weather and climate input parameters.
Data
Table
Column
Definition
End date of weather files

Maximum date for time
series
Minimum date of time
series
Number of precipitation
gages used
Precipitation laps rate
Cio
Gagedates
DATEF
MaxDate
End date of weather files

Maximum common date for time series type
Gagedates
MinDate
Minimum common date of time series type
Cio
NRGAGE
Sub
PLAPS
Rainfall distribution code
Cio
IDIST
Rainfall input
Cio
PCPSIM
Start date of weather

files
Weather input data
(overall)
Cio
DATES
Number of precipitation gage (.pcp) files used

in the simulation
Precipitation laps rate (millimetres
H2O/kilometre)
Rainfall distribution code
0: skewed distribution
1: mixed exponential distribution
Rainfall input code
1: measured data read for each sub basin
2: rainfall simulated/generated for each sub
basin
Start date of weather files
Wgn
(whole table)
This table contains weather input data.

Inclusive weather station(s).
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Input parameters: input data files created by SWAT saved in the TxtInOut folder
Below all input files in the TxtInOut folder are given.
The folder directory is:
SWAT Project name\Scenarios\Default (or scenario name)\TxtInOut
(in this case: Nsama, South Africa\Scenarios\ SWAT default scenario (present)\TxtInOut)
Table A4.13
The created input data files which are in the TxtInOut folder.
Data
File name
Extension
Full Name
Atmospheric deposition
Atmo.atm
.atm
Basin input data

Groundwater input data
HRU input data
Initial channel/reach dimensions
Input summary
Main channel/reach
Management input data
Master file
Precipitation
Reservoir input data
Soil chemical input data
Soil input data
Sub basin input data
Water Quality, sub basin level
Water Quality, watershed level
Watershed configuration
Weather input data
Basins.bsn
(sub basin and hru number).gw
(sub basin and hru number).hru
chan.deg
Input.std
(sub basin number).rte
(sub basin and hru number).mgt
File.cio
Pcp1.pcp
(sub basin number).res
(sub basin and hru number).chm
(sub basin and hru number).sol
(sub basin number).sub
(sub basin number).swq
Basins.wwq
Fig.fig
(sub basin number).wgn
.bsn
.gw
.hru
.deg
.std
.rte
.mgt
.cio
.pcp
.res
.chm
.sol
.sub
.swq
.wwq
.fig
.wgn
Watershed atmospheric
deposition file
Basin input file
Groundwater input file
HRU input file
Initial Channel Dimensions file
Input summary file
Main channel input file
Management input file
Master Watershed file
Precipitation input file
Reservoir input file
Soil chemical input file
Soil input file
Sub basin input file
Stream water quality input file
Watershed water quality file
Watershed configuration file
Weather generator input file
Input parameters: Self-made data files

Table A4.14
The self-made input data files.
Data
Folder
Name
PET
SWAT Project name\Scenarios\Default

(or scenario name)\TxtInOut
(in this case: Nsama, South
Africa\Scenarios\ SWAT default scenario
(present)\TxtInOut)
Tables input (self-made folder outside
SWAT Project Folder)
PET dayno.txt
Precipitation gage location

Precipitation values file
Weather generator gage location
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Alterra Report 2405
Precipitation Gage Location Table.dbf

(station name).dbf
(in this case study: B8E008.dbf)
Weather Generator Gage Location
Table.dbf
Output parameters: Files with results created by SWAT

Some of the output text files are copied into a database. The data in this database is not given in the tables
below. To be complete, the folder, the database file and the tables within this database are given below.
Folder within SWAT project: Scenarios\(saved scenario name)\TablesOut
(In this case study: (Nsama, South Africa\)Scenarios\ SWAT default scenario (present)\TablesOut)
Database file: SWATOutput.mdb
Tables: hru, rch, rsv, sed, sub and for all tables a table with the field definitions.
By tables A4.15 until A4.24:
Folder within SWAT project: Scenarios\(saved scenario name)\TxtInOut
(In this case study: (Nsama, South Africa\)Scenarios\SWAT default scenario (present)\TxtInOut)
Basin, HRU, Sub basin and Watershed

Table A4.15
The basin, HRU, sub basin en watershed output parameters.
Data
File
Column
Definition
Area of sub basin
Output.sub
AREA
Area of the sub basin

(kilometres2)
Hydrology and Water Quantity

Table A4.16
The hydrology and water quantity output parameters.
Data
File
Column
Definition
Drainage area of HRU
Output.hru
AREA
Drainage area of the HRU

(kilometres2)
Velocity in reach
Chanvel.out
CH_VEL
Water depth in reach
Watrdep.out
AVE WATER DEPTH
Velocity of water at each reach

(m/second)
Average water depth at each
reach (m)
Other Important Output Parameters

Table A4.17
Other important output parameters.
Data
File
Column
Definition
Output summary
Output.std
(whole file)
Output summary file
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63
Pesticides
Table A4.18
The pesticides output parameters.
Data
File
Column
Definition
Amount of pesticide(s) in river sediment
Output.rch
BED_PST
Amount of pesticide in surface runoff,

soluble in water
Amount of pesticide in surface runoff,
sorbed to sediment
Amount of pesticide(s) transported into
reservoir
Output.pst
SOLUBLE
Output.pst
SORBED
Output.rsv
PEST_IN
Amount of pesticide(s) transported out

of reservoir
Output.rsv
PEST_OUT
Average pesticide concentration in

reservoir sediment
Output.rsv
PSTCNCB
Average pesticide concentration in

reservoir water
Output.rsv
PSTCNCW
Name of pesticide modeled
Output.pst
PESTICIDE NAME
Pesticide loss through burying in

reservoir
Output.rsv
BURYPST
Pesticide loss through burying in river
Output.rch
BURYPST
Pesticide loss through reaction in

reservoir sediment
Output.rsv
REACBEDPST
Pesticide loss through reaction in river

sediment
Output.rch
REACBEDPST
Pesticide loss through reaction in

reservoir water
Output.rsv
REACTPST
Pesticide loss through reaction in river

water
Output.rch
REACTPST
Pesticide loss through volatilization in

reservoir
Output.rsv
VOLPST
Pesticide loss through volatilization in

river
Output.rch
VOLPST
Pesticide sorbed to river sediment

transported into reach
Output.rch
SORPST_IN
Pesticide in river bed sediment during time

step (milligrams active ingredient)
Amount of pesticide in solution in surface
runoff (milligrams)
Amount of pesticide sorbed to sediment in
surface runoff (milligrams)
Amount of pesticide transported into
reservoir during time step (milligrams active
ingredient)
Amount of pesticide transported out of
reservoir during time step (milligrams active
ingredient)
Average concentration of pesticide in
reservoir bed sediment during time step
(milligrams active ingredient/meter3 H2O
or ppb)
Average concentration of pesticide in
reservoir water during time step (milligrams
active ingredient/meter3 H2O or ppb)
Pesticide name from the database that was
used in the simulation
Loss of pesticide from reservoir sediment by
burial during time step (milligrams active
ingredient)
Loss of pesticide from river bed sediment by
burial during time step (milligrams active
ingredient)
Loss of pesticide from reservoir bed
sediment by reaction during time step
(milligrams active ingredient)
Loss of pesticide from river bed sediment by
reaction during time step (milligrams active
ingredient)
Loss of pesticide from water by reaction
during time step (milligrams active
ingredient)
Loss of pesticide from water by reaction
ingredient)
Loss of pesticide from water by volatilization
ingredient)
Loss of pesticide from water by volatilization
ingredient)
Pesticide sorbed to sediment transported
with water into reach during time step
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Alterra Report 2405
Table A4.18
(continuation): The pesticides output parameters.
Data
File
Column
Definition
Pesticide sorbed to river sediment

transported out of reach
Output.rch
SORPST_OUT
Pesticide transfer from reservoir

sediment to water by re-suspension
Output.rsv
RESUSP_PST
Pesticide transfer from river sediment

to water by re-suspension
Output.rch
RESUSP_PST
Pesticide transfer from water to

reservoir sediment by diffusion
Output.rsv
DIFFUSEPST
Pesticide transfer from water to river

sediment by diffusion
Output.rch
DIFFUSEPST
Pesticide transfer from water to

reservoir sediment by settling
Output.rsv
SETTLPST
Pesticide transfer from water to river

sediment by settling
Output.rch
SETTLPST
Soluble pesticide transported

into reach
Output.rch
SOLPST_IN
Soluble pesticide transported

out of reach
Output.rch
SOLPST_OUT
Pesticide sorbed to sediment transported

with water out of reach during time step
Transfer of pesticide from reservoir bed
sediment to water by re-suspension during
time step (milligrams active ingredient)
Transfer of pesticide from river bed
sediment to water by re-suspension during
time step (milligrams active ingredient)
Transfer of pesticide from water to reservoir
bed sediment by diffusion during time step
Transfer of pesticide from water to river bed
sediment by diffusion during time step
Transfer of pesticide from water to reservoir
bed sediment by settling during time step
Transfer of pesticide from water to river bed
sediment by settling during time step
Soluble pesticide transported with water into
reach during time step (milligrams active
ingredient)
Soluble pesticide transported with water out
of reach during time step (milligrams active
ingredient)
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65
Reaches
Table A4.19
The reach output parameters.
Data
File
Column
Definition
Area drained by reach

Evaporation of reach
Output.rch
Output.rch
AREA
EVAP
Stream flow into reach
Output.rch
FLOW_IN
Stream flow out of reach
Output.rch
FLOW_OUT
Water loss by transmission through the

streambed
Output.rch
TLOSS
Area drained by reach (kilometres2)

Average daily rate of water loss from reach
by evaporation during time step (m3/second)
Average daily stream flow into reach during
time step (m3/second)
Average daily stream flow out of reach
during time step (m3/second)
Average daily rate of water loss from reach
by transmission through the streambed
during time step (m3/second)
Data
File
Column
Definition
Flow into reservoir
Output.rsv
FLOW_IN
Flow out of reservoir
Output.rsv
FLOW_OUT
Volume of reservoir water
Output.rsv
VOLUME
Average flow into reservoir during time

step (m3/second H2O)
Average flow out of reservoir during time
step (m3/second H2O)
Volume of water in reservoir during time
step (m3 H2O)
Data
File
Column
Definition
Generated Runoff in HRU
output.hru
SURQ_GEN
Runoff contribution to stream flow in HRU output.hru
SURQ_CNT
Runoff contribution to stream flow in sub output.sub

basin
SURQ_CNT
Surface runoff generated in HRU during time

step (mm H2O)
Surface runoff contributed to stream flow in
the main channel during time step (mm H2O)
Surface runoff contribution to stream flow
during time step (mm H2O)
Reservoir
Table A4.20
The reservoir output parameters.
Surface Runoff
Table A4.21
The surface runoff output parameters.
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Water Balance
Table A4.22
The water balance output parameters.
Data
File
Column
Definition
Actual evapotranspiration at HRU

level
Actual evapotranspiration at sub
basin level
Deep aquifer recharge
Output.hru
ET
Output.sub
ET
Output.hru
DA_RCHG
Depth of water table measured

from above soil surface
Depth of water table measured
from
the bottom of the soil surface
Evaporation from reservoir
Groundwater contribution to
stream flow at HRU level
Output.hru
WTAB
Output.hru
WTABELO
Actual evapotranspiration from the HRU during time step

(mm H2O)
Actual evapotranspiration from the sub
basin during time step (mm H2O)
The amount of water from the root zone
that recharges the deep aquifer during
time step (mm H2O) (Shallow aquifer recharge = GW_RCHG
DA_RCHG)
Water table from above the soil surface
(mm)
Water table depth from the bottom of the soil surface (mm)
Output.rsv
Output.hru
EVAP
GW_Q
Evaporation from reservoir during time step (m3 H2O)

Water from the shallow aquifer that enters the main channel
during time step (mm H2O). Groundwater flow is also
referred to as
base flow.
Groundwater recharge
Output.hru
GW_RCHG
Initial soil water content at

HRU level
Output.hru
SW_INIT
Lateral flow contribution to stream

flow
Potential evapotranspiration at
HRU level
Potential evapotranspiration at
sub basin level
Percolation at HRU level
Output.hru
LATQ
Output.hru
PET
Output.sub
PET
Output.hru
PERC
Percolation at sub basin level
Output.sub
PERC
Re-evaporation
Output.hru
REVAP
Seepage of reservoir
Output.rsv
SEEPAGE
Soil water content at sub basin

level
Soil water content at the end of
time step at HRU level
Water stress of plant/crop
Output.sub
SW
Output.hru
SW_END
Output.hru
W_STRS
Total amount of water entering shallow and deep aquifers

In mm H2O. For the daily output, this column provides the
amount of water in the soil profile at the beginning of the
day. For the monthly and annual output, this is the average
soil water content for the time period (month or year)
Water flowing laterally within the soil profile that enters the
main channel during the time step (mm H2O).
Potential evapotranspiration from the HRU during time step
(mm H2O)
Potential evapotranspiration from the sub basin during time
step (mm H2O)
Water that percolates past the root zone during time step
(mm H2O)
Water that percolates past the root zone during time step
(mm H2O)
Water in the shallow aquifer returning to the root zone in
response to a moisture deficit during time step (mm H2O)
Water that seeps through the bottom of the reservoir and
enters the shallow aquifer during time step (m3 H2O)
Amount of water in the soil profile at the end of the time
period (mm H2O)
Amount of water in the soil profile at the end of the time
period (day, month or year) (mm H2O)
Water stress days during the time step (days)
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67
Water Quality
Table A4.23
The water quality and pesticides output parameters.
Data
File
Column
Definition
Clearness of reservoir water
output.rsv
SECHHIDEPTH
Secchi-disk depth of reservoir at end of time step (m)
Weather and Climate

Table A4.24
The weather and climate output parameters.
Data
File
Column
Definition
Rainfall at HRU
output.hru
PRECIP
Rainfall at reservoir
output.rsv
PRECIP
Rainfall at sub basin
output.sub
PRECIP
Total amount of precipitation falling on the HRU during

time step (mm H2O)
Precipitation falling directly on the reservoir during time
step (m3 H2O)
Total amount of precipitation falling on the sub basin
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Alterra Report 2405
Appendix 5 Tips and tricks for ArcSWAT
Microsoft Office 2010 (Excel) does not save a document as dbf-file anymore. The free software Open
Office (Calc) can save as dbf-file (downloadable from: www.openoffice.org).
Be sure your computer has the US setting, otherwise there are problems while editing input values.
Check if in the Data frame properties\Data frame\Clip options the option Clip to shape is selected and the
checkbox behind Clip grids and graticules is checked.
Dont adjust the environment of ArcGIS 10 before you have set up your SWAT project.
Put all input files in same coordinate system.
Dont store input tables inside your project folder (except PET file).
Dont remove maps from your ArcGIS 10 screen before completing the SWAT setup.
Dont forget to remove the outlets in the middle of the reservoir (when theres one in your project).
Adequate HRU thresholds (by step: HRU defining):

Land Use: 20%
Soil: 10%
Slope: 20%
Save the measured PET value input file in: (project name)\Scenarios\Default\TxtInOut
Be sure you have defined your weather station (user station) before writing the weather input file.
Editing SWAT input tables:

User Weather Stations
Reservoirs
For DDT modeling:
o General basin parameters
o Management
Be sure the 'pesticide application' is used! Do not use 'continuous pesticide'! Otherwise the
pesticide cant be routed through the stream reaches
o Routing parameters
o Soil chemical parameters
For changing land use:
o Land Use Update
The sensitivity analysis can take a long time.
Alterra Report 2405
69
70
Alterra Report 2405
Alterra is part of the international expertise organisation Wageningen UR (University & Research centre). Our mission
is To explore the potential of nature to improve the quality of life. Within Wageningen UR, nine research institutes
both specialised and applied have joined forces with Wageningen University and Van Hall Larenstein University of
Applied Sciences to help answer the most important questions in the domain of healthy food and living environment.
With approximately 40 locations (in the Netherlands, Brazil and China), 6,500 members of staff and 10,000 students,
Wageningen UR is one of the leading organisations in its domain worldwide. The integral approach to problems and
the cooperation between the exact sciences and the technological and social disciplines are at the heart of the
Wageningen Approach.
Alterra is the research institute for our green living environment. We offer a combination of practical and scientific
research in a multitude of disciplines related to the green world around us and the sustainable use of our living
environment, such as flora and fauna, soil, water, the environment, geo-information and remote sensing, landscape
and spatial planning, man and society.

using SWAT
Alterra Report 2405

ISSN 1566-7197
More information: www.wageningenUR.nl/en/alterra
E.P. Querner and M. van Zanen

Modelling Water Quantity and Quality Using SWAT

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Modelling Water Quantity and Quality Using SWAT

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Verfügbare Formate

Alterra is part of the international expertise organisation Wageningen UR (University & Research centre).

Modelling water quantity and quality

Alterra Report 2405

More information: www.wageningenUR.nl/en/alterra

E.P. Querner and M. van Zanen

Modelling water quantity and quality using SWAT

Modelling water quantity and quality

E.P. Querner1 and M. van Zanen2

Alterra Report 2405

Alterra Report 2405

Soil and Water Assessment Tool (SWAT)

Geographic information system ArcGIS10

Limpopo basin, South Africa

SWAT model building of Nsama sub basin

Aim of the modelling study

ArcSWAT interface to create model input data

Conclusions and recommendations

Appendix 1 Required steps in ArcGIS10 and SWAT

Appendix 2 ArcMap and ArcSWAT metadata of Project

Appendix 3 Results of the simulations

Appendix 4 Files with specific data

Appendix 5 Tips and tricks for ArcSWAT

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Aim of the modelling study

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Soil and Water Assessment Tool (SWAT)

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Geographic information system ArcGIS10

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The key procedures in ArcGIS to set up a SWAT application are:

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Limpopo basin, South Africa

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Description of the Nsama river basin

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Soils and relief

Soil (South African code) % of model area

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Closed shrub land

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Surface area of reservoir filled to emergency spillway (ha)

A is the surface area of the reservoir measured using Google Earth.

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SWAT model building of Nsama sub

ArcSWAT interface to create model input data

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Land use, soils and HRU units

Assumptions and other input data

Modelling present situation

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Results of the sensitivity analysis

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Initial SCS runoff curve number for moisture condition II

Description of the scenarios

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