U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2013–5002

Prepared in cooperation with the Iowa Department of Natural Resources

Use of the Soil and Water Assessment Tool (SWAT) for 

Simulating Hydrology and Water Quality in the Cedar 

River Basin, Iowa, 2000–10
Cover photograph: Cedar River at Seminole Valley Park, Cedar Rapids, Iowa.
Use of the Soil and Water Assessment 

Tool (SWAT) for Simulating Hydrology and 

Water Quality in the Cedar River Basin, 

Iowa, 2000–10

By Kasey Hutchinson and Daniel Christiansen

Prepared in cooperation with the Iowa Department of Natural Resources

Scientific Investigations Report 2013–5002

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Suzette M. Kimbal, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

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as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Hutchinson, K.J., and Christiansen, D.E., 2013, Use of the Soil and Water Assessment Tool (SWAT) for simulating 

hydrology and water quality in the Cedar River Basin, Iowa, 2000–10: U.S. Geological Survey Scientific Investigations 

Report 2013–5002, 36 p.
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Purpose and Scope ..............................................................................................................................2

Description of Study Area ...................................................................................................................2

Land Cover....................................................................................................................................2

Geology..........................................................................................................................................2

Climate...........................................................................................................................................7

Selected SWAT Studies in Iowa.........................................................................................................7

Methods.........................................................................................................................................................11

Model Description ..............................................................................................................................11

Model Input..........................................................................................................................................12

Subbasin Delineation .........................................................................................................................14

Model Calibration................................................................................................................................14

Statistical Evaluation of Model Performance .......................................................................14

Hydrology Calibration................................................................................................................18

Nitrate Load Calibration............................................................................................................18

Model Limitations.........................................................................................................................................20

Hydrology and Water Quality Simulation.................................................................................................21

Hydrology Calibration and Validation Results................................................................................21

Nitrate Calibration and Validation Results......................................................................................23

Alternative Hydrology Scenario Calibration and Validation ........................................................25

Summary........................................................................................................................................................32

References Cited..........................................................................................................................................33

Figures

1. Map showing location of the Cedar River Basin in Iowa and Minnesota...........................3

2. Map showing locations of U.S. Geological Survey streamflow-gaging stations, 

Iowa State University Ag Climate Network stations, National Weather Service 

Cooperative Observer Program stations, and Iowa Department of Natural Resources 

Storage and Retrieval/Water Quality Exchange stations providing measured data 

for the Cedar River Basin model, Iowa .....................................................................................6

3. Map showing National Agricultural Statistics Service 2008 Cropland Data Layer 

land-cover categories in the Cedar River Basin, Iowa ..........................................................8

4. Map showing landform regions of the Cedar River Basin, Iowa..........................................9

5. Map showing locations of selected Soil and Water Assessment Tool studies conducted in basins in Iowa............................................................................................................10

6. Map showing relative soil infiltration rates in the Cedar River Basin, Iowa ....................13

7. Map showing soil types likely to be drained in the Iowa part of the Cedar River 

Basin, Iowa ..................................................................................................................................15

8. Map showing percent slope for the Cedar River Basin model, Iowa................................16

9. Map showing subbasin delineation for the Cedar River Basin model, Iowa....................17
iv

10. Graphs showing calibration plots of measured and simulated monthly mean 

streamflow for each streamflow-gaging station in the Cedar River Basin model, 

Iowa ..............................................................................................................................................26

11. Graphs showing validation plots of measured and simulated monthly mean 

streamflow for each streamflow-gaging station in the Cedar River Basin model,

Iowa ..............................................................................................................................................27

Tables

1. Sites from which measured data were used for model set-up, calibration, and 

validation purposes for the Cedar River Basin model, Iowa.................................................4

2. Selected Soil and Water Assessment Tool (SWAT) studies conducted in basins 

in Iowa ............................................................................................................................................7

3. Management operation schedule for corn and soybeans for the Cedar River Basin 

model, Iowa .................................................................................................................................12

4. Soil and water assessment tool (SWAT) hydrology calibration parameters and 

parameter descriptions for the Cedar River Basin model, Iowa ........................................18

5. Soil and Water Assessment Tool final hydrology calibration values for the Cedar

 River Basin model, Iowa...........................................................................................................19

6. LOADEST statistical modeling results for each streamflow-gaging station for 

the Cedar River Basin model, Iowa, 2000–10 .........................................................................20

7. Soil and water assessment tool (SWAT) nitrate calibration parameters, parameter 

descriptions, and final calibration values for the Cedar River Basin model, Iowa..........20

8. Hydrology calibration (January 1, 2000, to December 31, 2004) results for each 

streamflow-gaging station for the Cedar River Basin model, Iowa...................................22

9. Hydrology validation (January 1, 2005, to December 31, 2010) results for each 

streamflow-gaging station for the Cedar River Basin model, Iowa...................................24

10. Nitrate load calibration (January 1, 2000, to December 31, 2004) and validation 

(January 1, 2005, to December 31, 2010) results for selected streamflow-gaging 

stations for the Cedar River Basin model, Iowa....................................................................25

11. List of streamflow-gaging stations used for the original and alternative scenario 

calibrations, and the streamflow-gaging stations used in place of the removed 

streamflow-gaging stations for calibration in the alternative scenario for the Cedar 

River Basin model, Iowa............................................................................................................28

12. Hydrology calibration (January 1, 2000, to December 31, 2004) results for each 

streamflow-gaging station for the alternative scenario for the Cedar River Basin 

model, Iowa .................................................................................................................................29

13. Hydrology validation (January 1, 2005, to December 31, 2010) results for each 

streamflow-gaging station for the alternative scenario for the Cedar River Basin 

model, Iowa .................................................................................................................................31
v

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2

)

acre 0.4047 hectare (ha)

acre 0.004047 square kilometer (km2

)

square mile (mi2

) 259.0 hectare (ha)

square mile (mi2

) 2.590 square kilometer (km2) 

Volume

cubic foot (ft3

) 0.02832 cubic meter (m3) 

Flow rate

cubic foot per second (ft3

/s) 0.02832 cubic meter per second (m3/s)

Application rate

pounds per acre per year 

[(lb/acre)/yr]

 1.121 kilograms per hectare per year 

[(kg/ha)/yr]

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows: 

°F=(1.8×°C)+32

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows: 

°C=(°F-32)/1.8

Abstract

The U.S. Geological Survey, in cooperation with the 

Iowa Department of Natural Resources, used the Soil and 

Water Assessment Tool to simulate streamflow and nitrate 

loads within the Cedar River Basin, Iowa. The goal was to 

assess the ability of the Soil and Water Assessment Tool to 

estimate streamflow and nitrate loads in gaged and ungaged 

basins in Iowa. The Cedar River Basin model uses measured 

streamflow data from 12 U.S. Geological Survey streamflowgaging stations for hydrology calibration. The U.S. Geological Survey software program, Load Estimator, was used to 

estimate annual and monthly nitrate loads based on measured 

nitrate concentrations and streamflow data from three Iowa 

Department of Natural Resources Storage and Retrieval/Water 

Quality Exchange stations, located throughout the basin, 

for nitrate load calibration. The hydrology of the model 

was calibrated for the period of January 1, 2000, to 

December 31, 2004, and validated for the period of 

January 1, 2005, to December 31, 2010. Simulated daily, 

monthly, and annual streamflow resulted in Nash-Sutcliffe 

coefficient of model efficiency (ENS) values ranging from 

0.44 to 0.83, 0.72 to 0.93, and 0.56 to 0.97, respectively, and 

coefficient of determination (R2

) values ranging from 0.55 

to 0.87, 0.74 to 0.94, and 0.65 to 0.99, respectively, for the 

calibration period. The percent bias ranged from -19 to 10, -16 

to 10, and -19 to 10 for daily, monthly, and annual simulation, 

respectively. The validation period resulted in daily, monthly, 

and annual ENS values ranging from 0.49 to 0.77, 0.69 to 0.91, 

and -0.22 to 0.95, respectively; R2 values ranging from 0.59 to 

0.84, 0.74 to 0.92, and 0.36 to 0.92, respectively; and percent 

bias ranging from -16 for all time steps to percent bias of 14, 

15, and 15, respectively. 

 The nitrate calibration was based on a small subset of 

the locations used in the hydrology calibration with limited 

measured data. Model performance ranges from unsatisfactory 

to very good for the calibration period (January 1, 2000, to 

December 31, 2004). Results for the validation period (January 1, 2005, to December 31, 2010) indicate a need for an 

increase of measured data as well as more refined documented 

management practices at a higher resolution. Simulated nitrate 

loads resulted in monthly and annual ENS values ranging from 

0.28 to 0.82 and 0.61 to 0.86, respectively, and monthly and 

annual R2 values ranging from 0.65 to 0.81 and 0.65 to 0.88, 

respectively, for the calibration period. The monthly and 

annual calibration percent bias ranged from 4 to 7 and 5 to 

7, respectively. The validation period resulted in all but two 

ENS values less than zero. Monthly and annual validation R2

values ranged from 0.5 to 0.67 and 0.25 to 0.48, respectively. 

Monthly and annual validation percent bias ranged from 46 to 

68 for both time steps. A daily calibration and validation for 

nitrate loads was not performed because of the poor monthly 

and annual results; measured daily nitrate data are available 

for intervals of time in 2009 and 2010 during which a successful monthly and annual calibration could not be achieved. 

The Cedar River Basin is densely gaged relative to other 

basins in Iowa; therefore, an alternative hydrology scenario 

was created to assess the predictive capabilities of the Soil 

and Water Assessment Tool using fewer locations of measured 

data for model hydrology calibration. Although the ability of 

the model to reproduce measured values improves with the 

number of calibration locations, results indicate that the Soil 

and Water Assessment Tool can be used to adequately estimate 

streamflow in less densely gaged basins throughout the State, 

especially at the monthly time step. However, results also indicate that caution should be used when calibrating a subbasin 

that consists of physically distinct regions based on only one 

streamflow-gaging station. 

Introduction

An extensive network of U.S. Geological Survey (USGS) 

streamflow-gaging stations spans the State of Iowa, and 

although hydrologic information for these streamflow-gaging 

stations is provided on a near real-time basis, there is still a 

need for hydrologic information at ungaged locations. The 

USGS, in cooperation with the Iowa Department of Natural 

Resources (IDNR), conducted a study to estimate streamflow 

and nutrient loading at any point on a stream by developing a 

Use of the Soil and Water Assessment Tool (SWAT) for 

Simulating Hydrology and Water Quality in the Cedar River 

Basin, Iowa, 2000–10

By Kasey Hutchinson and Daniel Christiansen
2 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

comprehensive approach using predictive tools and modeling. 

The ability to estimate streamflow and water quality can provide valuable information for environmental studies, hydraulic 

design, reservoir management, water management, urban studies, and recreation. This study focuses on the use of the Soil 

and Water Assessment Tool (SWAT) (Arnold and others, 1998; 

Neitsch and others, 2005) for making such estimates. The 

availability of varied and extensive land-management options 

in SWAT make it an ideal model for simulating streamflow 

and chemical fate and transport in agricultural basins.

While the scope of the project is statewide, the Cedar 

River Basin, located in central Iowa, was selected as the first 

basin to be modeled (fig. 1). Agriculture dominates land cover 

in the basin in the form of row crops, and artificial drainage 

is extensive (Iowa Department of Natural Resources, 2006a). 

The basin was removed from the State’s 303(d) list for nitratenitrogen in 2008 because of Total Maximum Daily Load 

(TMDL) approval, but remains on the list for bacteria (Iowa 

Department of Natural Resources, 2008a), biological, low dissolved oxygen, mercury, and polychlorinated biphenyl (PCB) 

impairments (Iowa Department of Natural Resources, 2010a). 

Purpose and Scope 

This report describes the SWAT results of hydrology and 

water quality simulation, specifically the hydrology and nitrate 

load calibration (January 1, 2000, to December 31, 2004) and 

hydrology and nitrate load validation (January 1, 2005, to 

December 31, 2010) for the Cedar River Basin. The ability of 

SWAT to simulate streamflow and nitrate loads for the Cedar 

River Basin was tested as was the potential for making the 

same estimates for ungaged stream reaches in Iowa. This 

was done by creating an alternative scenario in which the 

model was calibrated and validated using only a subset of the 

streamflow-gaging stations used in the initial calibration and 

validation. The alternative scenario can indicate the level of 

reliability of SWAT to accurately predict streamflow in less 

densely gaged basins, which is more typical of other basins in 

the State. Model limitations were investigated and described. 

Description of Study Area

Draining approximately 7,815 square miles, the Cedar 

River Basin extends from its headwaters in southern Minnesota to its outlet in southeastern Iowa at Columbus Junction 

where it joins, as the largest tributary, the Iowa River, (fig. 1) 

(Iowa Department of Natural Resources, 2006a; Squillace and 

others, 1996). Row-crop agriculture dominates the land cover 

in the form of corn and soybeans, and the basin is extensively 

artificially drained (Iowa Department of Natural Resources, 

2006a). Artificial drainage includes open ditches and subsurface drainage tile, both designed to remove excess water 

from the soil subsurface. Confined and unconfined livestock 

operations that include beef and dairy cattle, hogs, sheep, and 

poultry are located throughout the basin (Iowa Department 

of Natural Resources, 2006a). Designated uses for the Cedar 

River include primary contact recreation, significant resource 

warm water, and drinking water supply (Iowa Department of 

Natural Resources, 2006a). There are 12 USGS streamflowgaging stations, 3 IDNR Storage and Retrieval/Water Quality 

Exchange (STORET/WQX) stations, 4 Iowa State University 

(ISU) Ag Climate Network stations, and 22 National Weather 

Service (NWS) Cooperative Observer Program (COOP) stations, located within and surrounding the basin from which 

measured data have been acquired for this study (fig. 2, 

table 1). 

Land Cover 

The U.S. Department of Agriculture (USDA), National 

Agricultural Statistics Service (NASS) 2008 Cropland Data 

Layer (CDL) (National Agricultural Statistics Service, 2008) 

was acquired and assessed to estimate land-cover types. The 

SWAT hydrologic response unit (HRU) definition tool was 

used to process the data and a threshold value was set so 

that land-cover types that occupied less than 5 percent of a 

subbasin were eliminated, with the remaining land-cover types 

being reapportioned to account for all of the land area of 

the subbasin. This resulted in row crops dominating the basin 

at 76 percent of the total land area, with 44 percent corn and 

32 percent soybeans. The remaining basin land area is comprised of pasture at 11 percent, roadway at 8 percent, forested 

lands at 2 percent, and water, wetland, and developed land 

combined at 3 percent (fig. 3). The two largest urban areas in 

the basin include Waterloo and Cedar Rapids, Iowa (fig. 1), 

with smaller urban areas scattered throughout the basin.

Geology 

The upper bedrock of the Cedar River Basin consists of 

Ordovician-age sandstone and dolostone, Silurian dolomites, 

and Devonian-age limestones (Squillace and others, 1996); 

the Silurian-Devonian and Ordovician systems are important 

aquifers within the basin and are used extensively for municipal, domestic, and industrial water supplies (Iowa Department 

of Natural Resources, 2006a; Squillace and others, 1996). 

Karst features that include caves, springs, and sinkholes, are 

prevalent in the northern part of the basin (Prior, 1991; Iowa 

Department of Natural Resources, 2006a). These conduits in 

the shallow bedrock can decrease and delay high peak flows, 

sustain flow during dry periods, and provide direct conduits 

for delivery of nitrate to aquifers (Baffaut and Benson, 2009; 

Iowa Department of Natural Resources, 2006a; Prior, 1991). 

Four distinct landform regions comprise the Cedar River Basin 

and include the Iowan Surface, the Southern Iowa Drift Plain, 

the Des Moines Lobe, and Iowa-Cedar Lowland (Prior, 1991; 

fig. 4). The Iowan Surface, primarily glacial drift with thin 

loess layers on ridges, makes up the eastern part of the basin. 
Introduction 3

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93°

94°

92°

91°

91°

44°

43°

42°

STEELE

COUNTY

DODGE

COUNTY

MITCHELL

COUNTY

WORTH

COUNTY

TAMA

COUNTY

WINNEBAGO

COUNTY

BUTLER

COUNTY

FRANKLIN

COUNTY

BENTON

COUNTY

MOWER COUNTY

WRIGHT

COUNTY

HANCOCK

COUNTY

BREMER

COUNTY

MARSHALL

COUNTY

IOWA COUNTY

FREEBORN COUNTY

CERRO

GORDO

COUNTY

FLOYD

COUNTY

BUCHANAN

COUNTY

BLACK HAWK

COUNTY

JONES

COUNTY

FERIBAULT

COUNTY

CHICKASAW

COUNTY

HOWARD

COUNTY

GRUNDY

COUNTY

HARDIN

COUNTY

LINN

COUNTY

MUSCATINE

COUNTY

SCOTT COUNTY

LOUISA

COUNTY

CEDAR

COUNTY

JOHNSON

COUNTY

EXPLANATION

Cedar River Basin boundary

MINNESOTA

IOWA

Cedar

Rapids

Waterloo

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Cedar River

Mason City

Ionia

Janesville

New

Hartford

Hudson

Dysart

Conesville

Austin

Finchford

Columbus 

Junction

IOWA

MINNESOTA

Study area

elttiL 

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

Shell Rock

Janesville

Finchford

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

IOWA

ILLINOIS

Base from U.S. Geological Survey digital data, variously 

dated, various scales

Universal Transverse Mercator projection, Zone 15

North Amercian Datum of 1983

Figure 1. Location of the Cedar River Basin in Iowa and Minnesota. 
4 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin Table 1. Sites from which measured data were used for model set-up, calibration, and validation purposes for the Cedar River Basin model, Iowa. [STORET/WQX, Storage and Retrieval/Water Quality Exchange; min, minimum; max, maximum] Map number (fig. 2) Network Site ID number Site name and location Measured parameter

1 U.S. Geological Survey 05457000 Cedar River near Austin, Minnesota Streamflow.

2 U.S. Geological Survey 05459500 Winnebago River at Mason City, Iowa Streamflow.3 U.S. Geological Survey 05458000 Little Cedar River near Ionia, Iowa Streamflow.4 U.S. Geological Survey 05462000 Shell Rock River at Shell Rock, Iowa Streamflow.5 U.S. Geological Survey 05458900 West Fork Cedar River at Finchford, 

Iowa

Streamflow.

6 U.S. Geological Survey 05458500 Cedar River at Janesville, Iowa Streamflow.7 U.S. Geological Survey 05463000 Beaver Creek at New Hartford, Iowa Streamflow.8 U.S. Geological Survey 05464000 Cedar River at Waterloo, Iowa Streamflow.9 U.S. Geological Survey 05463500 Black Hawk Creek at Hudson, Iowa Streamflow.

10 U.S. Geological Survey 05464220 Wolf Creek near Dysart, Iowa Streamflow.

11 U.S. Geological Survey 05464500 Cedar River at Cedar Rapids, Iowa Streamflow.

12 U.S. Geological Survey 05465000 Cedar River near Conesville, Iowa Streamflow.

13 Iowa Department of Natural Resources STORET/WQX 10120001 Shell Rock River at Shell Rock, Iowa Nitrite + Nitrate.

14 Iowa Department of Natural Resources STORET/WQX 10090001 Cedar River at Janesville, Iowa Nitrite + Nitrate.

15 Iowa Department of Natural Resources STORET/WQX 10700001 Cedar River near Conesville, Iowa Nitrite + Nitrate.

16 Iowa State University Ag Climate A134309 Kanawha, Iowa Solar Radiation, Wind Speed, Relative Humidity.

17 Iowa State University Ag Climate A135879 Nashua, Iowa Solar Radiation, Wind Speed, Relative Humidity.

18 Iowa State University Ag Climate A131329 Cedar Rapids, Iowa Solar Radiation, Wind Speed, Relative Humidity.

19 Iowa State University Ag Climate A135849 Muscatine, Iowa Solar Radiation, Wind Speed, Relative Humidity.

20 National Weather Service Cooperative Observer Program 210355 Austin, Minnesota Precipitation, Max/Min Temperature.

21 National Weather Service Cooperative Observer Program 210075 Albert Lea, Minnesota Precipitation, Max/Min Temperature.

22 National Weather Service Cooperative Observer Program 136103 Northwood, Iowa Precipitation, Max/Min Temperature.

23 National Weather Service Cooperative Observer Program 132977 Forest City, Iowa Precipitation, Max/Min Temperature.

24 National Weather Service Cooperative Observer Program 136305 Osage, Iowa Precipitation, Max/Min Temperature.

25 National Weather Service Cooperative Observer Program 135230 Mason City, Iowa Precipitation, Max/Min Temperature.

26 National Weather Service Cooperative Observer Program 131402 Charles City, Iowa Precipitation, Max/Min Temperature.

27 National Weather Service Cooperative Observer Program 135952 New Hampton, Iowa Precipitation, Max/Min Temperature.

28 National Weather Service Cooperative Observer Program 133584 Hampton, Iowa Precipitation, Max/Min Temperature.
Introduction 

5

29 National Weather Service Cooperative Observer Program 130157 Allison, Iowa Precipitation, Max/Min Temperature.

30 National Weather Service Cooperative Observer Program 134142 Iowa Falls, Iowa Precipitation, Max/Min Temperature.

31 National Weather Service Cooperative Observer Program 138706 Waterloo, Iowa Precipitation, Max/Min Temperature.

32 National Weather Service Cooperative Observer Program 132573 Eldora, Iowa Precipitation, Max/Min Temperature.

33 National Weather Service Cooperative Observer Program 133487 Grundy Center, Iowa Precipitation, Max/Min Temperature.

34 National Weather Service Cooperative Observer Program 134049 Independence, Iowa Precipitation, Max/Min Temperature.

35 National Weather Service Cooperative Observer Program 138568 Vinton, Iowa Precipitation, Max/Min Temperature.

36 National Weather Service Cooperative Observer Program 130600 Belle Plain, Iowa Precipitation, Max/Min Temperature.

37 National Weather Service Cooperative Observer Program 131319 Cedar Rapids, Iowa Precipitation, Max/Min Temperature.

38 National Weather Service Cooperative Observer Program 130213 Anamosa, Iowa Precipitation, Max/Min Temperature.

39 National Weather Service Cooperative Observer Program 134101 Iowa City, Iowa Precipitation, Max/Min Temperature.

40 National Weather Service Cooperative Observer Program 138266 Tipton, Iowa Precipitation, Max/Min Temperature.

41 National Weather Service Cooperative Observer Program 135837 Muscatine, Iowa Precipitation, Max/Min Temperature.

Table 1. Sites from which measured data were used for model set-up, calibration, and validation purposes for the Cedar River Basin model, Iowa. [STORET/WQX, Storage and Retrieval/Water Quality Exchange; min, minimum; max, maximum]

Map 

number 

(fig. 2)

Network Site ID number Site name and location Measured parameter
6 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Figure 2. Locations of U.S. Geological Survey streamflow-gaging stations, Iowa State University Ag Climate Network 

stations, National Weather Service Cooperative Observer Program stations, and Iowa Department of Natural Resources 

Storage and Retrieval/Water Quality Exchange stations providing measured data for the Cedar River Basin model, Iowa. 

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93°

94°

92°

91°

91°

44°

43°

42°

STEELE

COUNTY

DODGE

COUNTY

MITCHELL

COUNTY

WORTH

COUNTY

TAMA

COUNTY

WINNEBAGO

COUNTY

BUTLER

COUNTY

FRANKLIN

COUNTY

BENTON

COUNTY

MOWER COUNTY

WRIGHT

COUNTY

HANCOCK

COUNTY

BREMER

COUNTY

MARSHALL

COUNTY

IOWA COUNTY

FREEBORN COUNTY

CERRO

GORDO

COUNTY

FLOYD

COUNTY

BUCHANAN

COUNTY

BLACK HAWK

COUNTY

JONES

COUNTY

FERIBAULT

COUNTY

CHICKASAW

COUNTY

HOWARD

COUNTY

GRUNDY

COUNTY

HARDIN

COUNTY

LINN

COUNTY

MUSCATINE

COUNTY

SCOTT COUNTY

LOUISA

COUNTY

CEDAR

COUNTY

JOHNSON

COUNTY

21

20

1

36

9

6

37

25

33

8

4

23

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3

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24

38

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34

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30

26

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10

14

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18

16 17

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12

11

15

EXPLANATION

MINNESOTA Cedar River Basin boundary

IOWA

Cedar River

elttiL 

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

IOWA

ILLINOIS

U.S. Geological Survey streamflow-gaging station 

and site identifier (table 1)

Iowa Department of Natural Resources Storage 

and Retrieval/Water Quality Exchange station 

sample site and site identifier (table 1)

Iowa State University Ag Climate Network station 

and site identifier (table 1)

National Weather Service Cooperative Observer 

Program station and site identifier (table 1) 

1

13

16

20

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Base from U.S. Geological Survey digital data, variously 

dated, various scales

Universal Transverse Mercator projection, Zone 15

North Amercian Datum of 1983
Introduction 7

It is characterized by long slopes, low relief, and well developed drainage (Prior, 1991). The Southern Iowa Drift Plain, 

which is predominantly glacial drift and loess, makes up the 

southern part of the basin. It is characterized by steeply rolling 

terrain, moderately well-drained soils, and broad, flat drainage 

divides (Prior, 1991). The Des Moines Lobe in the western 

part of the basin is characterized by poorly drained soils 

and low local relief with some distinct ridges. The dominant 

surficial material is glacial till with alluvium along the streams 

(Prior, 1991). The Iowa-Cedar Lowland (fig. 4), formerly part 

of the Alluvial Plains landform region, is located at the southern end of the basin at the confluence of the Cedar and Iowa 

Rivers (Iowa Department of Natural Resources, 2009). 

Climate 

Daily temperature and precipitation data from 22 NWS 

COOP stations located throughout and surrounding the basin 

were collected from January, 1, 1978, to December 21, 2010 

(National Weather Service Cooperative Observer Program, 

2001–12, 2009), for calculating statistical values of daily precipitation and temperature data for use in the SWAT weather 

generator. Average annual temperature, determined using data 

from stations located within the basin boundary (14 in total), 

ranges from 45 degrees Fahrenheit (oF) in the northern part 

of the basin to 48 oF in the southern part. The average annual 

precipitation ranges from 33.67 to 35.85 inches. The period 

of January, 1, 2000, to December 21, 2010, was selected for 

simulation, during which the average annual temperature and 

precipitation ranged from 45 oF to 48 oF and 33.89 to 38.20 

inches, respectively. 

Selected SWAT Studies in Iowa 

Multiple SWAT studies have been done for Iowa basins 

(fig. 5, table 2) with a large focus on water budget and nutrient transport in agriculturally-dominated, artificially drained 

basins. Iowa has been identified as exporting some of the largest amounts of nitrates in the Midwest (Kalkhoff and others, 

2001). Schilling and Libra (2000) estimated that 25 percent 

of the average annual nitrate delivered to the Gulf of Mexico 

is exported from Iowa. Many studies indicate that subsurface 

tile drainage increases nitrate losses from the basin by way of 

enhanced leaching through the soil profile with subsequent 

direct routing to surface water, often exceeding the U.S. Environmental Protection Agency (USEPA) drinking water regulation of 10 mg/L (David and others, 1997; Gilliam and others, 

1999; Kladivko and others, 2004; Jaynes and others, 2001; Hu 

and others, 2007; Sui and Frankenberger, 2008). Subsurface 

tile drainage also has a profound effect on the hydrology of 

a basin (Eidem, and others, 1999; Jaynes, and others, 1999; 

Green and others, 2006), and becomes an essential component when balancing the hydrologic pathways (Kannan and 

others, 2006; Green and others, 2006; Saleh and others, 2007). 

Multiple factors such as fertilization rate and timing, soil type, 

drainage conditions, soil nitrogen content, drain-tile spacing 

and depth, and cropping systems affect nutrient dynamics 

(Randall and Goss, 2001; Gollamudi and others, 2007). Many 

studies have used SWAT because of its physical representation 

capabilities in conjunction with varied management options 

and a tile-drainage simulation component (Gollamudi and others, 2007). 

Reungsang and others (2005) evaluated SWAT to simulate hydrology and nitrate levels in the Upper Maquoketa 

River Basin, located in northeast Iowa. The results of the 

study indicated that streamflow and nitrate as N loads could 

Table 2. Selected Soil and Water Assessment Tool (SWAT) studies conducted in basins in Iowa. 

[LSNT, late-spring nitrate test; FEM, farm-level economic model]

Study title Authors Study area (major basin)

Calibration and validation of SWAT for the Upper Maquoketa 

River watershed

Reungsang and others, 2005 Upper Maquoketa River (Maquoketa 

River Basin).

Evaluation of SWAT in simulating nitrate nitrogen and atrazine 

fates in a watershed with tiles and potholes

Du and others, 2006 Walnut Creek (Skunk River Basin).

Hydrologic evaluation of the soil and water assessment tool for a 

large tile-drained watershed in Iowa

Green and others, 2006 South Fork River (Iowa River 

Basin).

Water quality modeling for the Raccoon River watershed using 

SWAT

Jha and others, 2007 Raccoon River (Raccoon River 

Basin).

Economic and environmental impacts of LSNT and cover crops 

for nitrate-nitrogen reduction in Walnut Creek Watershed, Iowa, 

using FEM and enhanced SWAT models

Saleh and others, 2007 Walnut Creek Watershed (Skunk 

River Basin).

Modeling nitrate-nitrogen load reduction strategies for the Des 

Moines River, Iowa using SWAT

Schilling and Wolter, 2009 Des Moines River (Des Moines 

River Basin).

Targeting land-use change for nitrate-nitrogen load reductions in an 

agricultural watershed

Jha and others, 2010 Squaw Creek (Skunk River Basin).
8 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Figure 3. National Agricultural Statistics Service 2008 Cropland Data Layer land-cover categories in the Cedar River 

Basin, Iowa.

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93°

94°

92°

91°

91°

44°

43°

42°

STEELE

COUNTY

DODGE

COUNTY

MITCHELL

COUNTY

WORTH

COUNTY

TAMA

COUNTY

WINNEBAGO

COUNTY

BUTLER

COUNTY

FRANKLIN

COUNTY

BENTON

COUNTY

MOWER COUNTY

WRIGHT

COUNTY

HANCOCK

COUNTY

BREMER

COUNTY

MARSHALL

COUNTY

IOWA COUNTY

FREEBORN COUNTY

CERRO

GORDO

COUNTY

FLOYD

COUNTY

BUCHANAN

COUNTY

BLACK HAWK

COUNTY

JONES

COUNTY

FERIBAULT

COUNTY

CHICKASAW

COUNTY

HOWARD

COUNTY

GRUNDY

COUNTY

HARDIN

COUNTY

LINN

COUNTY

MUSCATINE

COUNTY

SCOTT COUNTY

LOUISA

COUNTY

CEDAR

COUNTY

JOHNSON

COUNTY

EXPLANATION

Cedar River Basin boundary

MINNESOTA

IOWA

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Cedar River

elttiL

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

Cedar RiverCedar River

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

IOWA

ILLINOIS

elttiL

Land-cover category

Corn

Soybean

Pasture

Forested

Wetland

Water

Roadway/developed

Base from U.S. Geological Survey digital data, variously 

dated, various scales

Universal Transverse Mercator projection, Zone 15

North Amercian Datum of 1983

Land-use data modified from the U.S. Department of

Agriculture-National Agricultural Statistics Service,

Cropland Data Layer, 2008
Introduction 9

Figure 4. Landform regions of the Cedar River Basin, Iowa.

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93°

94°

92°

91°

91°

44°

43°

42°

STEELE

COUNTY

DODGE

COUNTY

MITCHELL

COUNTY

WORTH

COUNTY

TAMA

COUNTY

WINNEBAGO

COUNTY

BUTLER

COUNTY

FRANKLIN

COUNTY

BENTON

COUNTY

MOWER COUNTY

WRIGHT

COUNTY

HANCOCK

COUNTY

BREMER

COUNTY

MARSHALL

COUNTY

IOWA COUNTY

FREEBORN COUNTY

CERRO

GORDO

COUNTY

FLOYD

COUNTY

BUCHANAN

COUNTY

BLACK HAWK

COUNTY

JONES

COUNTY

FERIBAULT

COUNTY

CHICKASAW

COUNTY

HOWARD

COUNTY

GRUNDY

COUNTY

HARDIN

COUNTY

LINN

COUNTY

MUSCATINE

COUNTY

SCOTT COUNTY

LOUISA

COUNTY

CEDAR

COUNTY

JOHNSON

COUNTY

MINNESOTA

IOWA

Cedar RiverCedar River

elttiL 

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

IOWA

ILLINOIS

EXPLANATION

Cedar River Basin boundary

Des Moines Lobe

Iowan Surface

Southern Iowa Drift Plain

Iowa-Cedar Lowland

Landform region data modified from the 

Iowa Department of Natural Resources, 

The Landform Regions of Iowa, 2009

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Base from U.S. Geological Survey digital data, variously 

dated, various scales

Universal Transverse Mercator projection, Zone 15

North Amercian Datum of 1983
10 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Base from U.S. Geological Survey National Atlas of the United States digital data, 1:2,000,000, 

Iowa Department of Natural Resources digital data, 1:24,000 

Universal Transverse Mercator projection, Zone 15 

North American Datum of 1983

96° 94° 92° 90°

44°

42°

0 50 100 MILES

0 50 100 KILOMETERS

Upper Maquoketa River

(Maquoketa River Basin)

South Fork River (Iowa River Basin)

Squaw Creek (Skunk River Basin)

Walnut Creek (Skunk River Basin)

Des Moines River (Des Moines River Basin) 

Raccoon River 

(Raccoon River Basin)

Study area boundary

IOWA

MINNESOTA

WISCONSIN

ILLINOIS

NEBRASKA

MISSOURI

SOUTH

DAKOTA

EXPLANATION

Figure 5. Locations of selected Soil and Water Assessment Tool studies conducted in basins in Iowa. 
Methods 11

be replicated successfully by SWAT for the Upper Maquoketa River Basin. The study also illustrated the importance of 

climate inputs for model validation; results improved when 

a subset of the climate stations located within the basin were 

selected for climate data inputs. 

Du and others (2006) evaluated SWAT in simulating 

nitrate and atrazine fates in the Walnut Creek Basin, a heavily artificially-drained agricultural basin located in the South 

Skunk River Basin in central Iowa. They compared an earlier 

version of SWAT (SWAT2000) with an upgraded version 

(SWAT-M) (Du and others, 2005) that incorporated tile drainage simulation, to assess the overall performance of SWAT, as 

well as the ability of the model to simulate subsurface flow. 

Simulation results improved with the modified version, and 

subsurface nitrate loads were reasonably simulated. Other 

SWAT work in Walnut Creek includes a study conducted by 

Saleh and others (2007) evaluating multiple best management 

practice scenarios for reducing nutrient and sediment loadings. Model simulations incorporating use of the late-spring 

nitrate test, cover crops, and a combination of the two methods 

reduced nutrient and sediment loadings from the basin.

Green and others (2006) evaluated the ability of SWAT to 

simulate hydrology in the South Fork River watershed of the 

Iowa River Basin located in central Iowa, an agricultural basin 

with extensive tile drainage. They determined that simulations 

with a tile flow component resulted in a water yield of 

25.1 percent of precipitation, while simulations without a 

tile flow component resulted in 16.9 percent of precipitation. 

The tile flow scenario produced reasonable water-budget 

components, indicating that SWAT can be used for simulating tile flow and evaluating different management practices in 

agricultural basins. 

Jha and others (2007) assessed the water quality of the 

Raccoon River Basin, an agricultural basin with substantial 

amounts of artificial drainage located in west-central Iowa. In 

their study, SWAT was calibrated and validated for streamflow, sediment, and nutrient loadings. The results of shifts 

in land-cover and management practices on loadings also 

were assessed. The model successfully predicted annual and 

monthly streamflow, as well as sediment, nitrate, organic nitrogen, organic phosphorus (P), and mineral P. 

Schilling and Wolter (2009) used SWAT to evaluate 

nitrate-reduction strategies, including different spatial configurations, for TMDL purposes for the Des Moines River Basin in 

north-central Iowa. Their simulations indicated that reducing 

fertilizer application rates could achieve the required TMDL 

nitrate reduction; the most efficient simulated load reduction was achieved when targeting subbasins near the outlet 

of the basin, while the greatest simulated load reduction was 

achieved by targeting the highest yielding subbasins. 

Jha and others (2010) used SWAT to evaluate the effects 

of four different land-use scenarios on nitrate loads in the 

Squaw Creek Basin, an agricultural basin and tributary of the 

South Skunk River in south-central Iowa. Their simulations 

indicated that targeting row crops on highly erodible land and 

headwater areas could provide efficient solutions for reducing 

nitrate loads. They also determined that targeting floodplains 

for grassland conversion did not prove to be as effective of an 

approach for reducing nitrate loads. 

Methods

Model Description

SWAT, developed by the USDA Agricultural Research 

Service (ARS), is a physically-based, continuous time model 

that is designed to assess the effect of management and 

climate change on water, sediment, and agricultural chemical 

yields over long periods of time (Arnold and Fohrer, 2005; Jha 

and others, 2007; Gassman and others, 2007). The ArcGISArcView extension ArcSWAT allows for the SWAT model to 

be executed within a geographic information system (GIS), 

and provides tools for developing and running the model 

(Gassman and others, 2007; Saleh and others, 2007). 

SWAT can run at variable time steps and uses readilyavailable land-cover, climatic, soils, and topographic input 

data for simulating water budget, sediment yield, and nutrient fluxes (Gassman and others, 2007; Hu and others, 2007). 

Major components incorporated into the model include 

weather, hydrology, soil properties, land management, erosion, sediment transport, plant growth, nutrient and pesticide 

loading, bacteria transport, irrigation, and pond and reservoir 

storage (Gassman and others, 2007; Green and others, 2006). 

Hydrologic and climatic processes include precipitation, 

evapotranspiration, infiltration, surface runoff, groundwater flow, shallow aquifer flow, return flow, and transmission 

losses. 

Input to SWAT is applied at different levels of detail 

that include the basin, subbasin, and HRU. The basin is first 

delineated into subbasins with each subbasin identified by a 

single reach (Garcia, 2009). Subbasins can be further delineated into HRUs, which consist of homogeneous land cover, 

management, and soil characteristics (Gassman and others, 

2007). The HRUs are not represented spatially in SWAT but 

rather are percentages of the subbasins based on the unique 

combinations of characteristics (Gassman and others, 2007). 

The amount of water, sediment, nutrient, and pesticide loadings delivered to the main reach is calculated separately for 

each HRU and then summed to determine total subbasin water 

yield and constituent loadings (Neitsch and others, 2005). The 

resulting water yield and loads are then allocated to the corresponding subbasin reach of each subbasin, which then exit 

the subbasin at the outlet (Garcia, 2009). On delivery to the 

main channel, discharges and fluxes are kinematically routed 

downstream and chemical transformations are simulated in the 

stream and streambed, dividing this phase into water, sediment, nutrients, and organic chemicals (Garcia, 2009, Neitsch 

and others, 2005). Model output is provided for each subbasin 

outlet, including the designated whole-basin outlet. 
12 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Model Input 

SWAT model version SWAT2009.exe revision 480 was 

used for this study. The ArcGIS 9.3.1 (Environmental Systems Research Institute, 2009) extension ArcSWAT version 

2009.93.5 (Winchell and others, 2010) was used for model 

input generation and processing, which required incorporation 

of digital datasets representing elevation, land cover, soils, and 

climate. A digital elevation model was derived for Minnesota 

and Iowa from the USGS 30-m National Elevation Dataset 

(NED) (U.S. Geological Survey, 2009). The 2008 CDL from 

the USDA-NASS (National Agricultural Statistics Service, 

2008), which contains crop-specific digital data layers, was 

used to describe land cover, allowing land cover to be categorized into specific agricultural land cover as compared to 

generic designations. The Soil Survey Geographic Database 

(SSURGO) from the USDA Natural Resources Conservation 

Service (NRCS) (Natural Resources Conservation Service, 

2009) was used as soils input, providing detailed properties 

and distribution of soils in the study area. The hydrologic soils 

group, one of the SSURGO data attributes, represents relative infiltration rate of a soil (fig. 6) and is used in the NRCS 

curve-number (CN) method (Soil Conservation Service, 1986) 

for estimating surface runoff. Daily precipitation and maximum and minimum temperature data were obtained for 20 

NWS COOP stations from the ISU, Department of Agronomy, 

Iowa Environmental Mesonet (IEM) (National Weather 

Service Cooperative Observer Program, 2001–12) for Iowa 

locations and for two NWS COOP stations from the National 

Climatic Data Center (National Weather Service Cooperative Observer Program, 2009) for Minnesota locations. Daily 

solar radiation, wind speed, and relative humidity data were 

obtained for four ISU Ag climate stations, provided by IEM 

(High Plains Regional Climate Center, 2001–12). 

Average monthly nitrate loads for point sources were estimated for National Pollutant Discharge Elimination System 

(NPDES) permitted facilities in the basin (Iowa Department 

of Natural Resources, 2006a). Some discharge monitoring 

data and affiliated nitrate load estimates were provided by 

the IDNR (F. Amin, Iowa Department of Natural Resources, 

written and oral commun., 2010; L. Bryant, Iowa Department of Natural Resources, written and oral commun., 2010). 

Many of the facilities did not have available permit data; the 

Cedar River TMDL for nitrate (Iowa Department of Natural 

Resources, 2006a) report and the Total Maximum Daily Load 

for Escherichia coli (E. coli) report (U.S. Environmental 

Protection Agency, 2010) were used as guides for estimating 

total nitrogen effluent from each facility, from which nitrate 

loads were estimated for input into SWAT. In the absence 

of IDNR provided estimates, the design limit was used for 

facilities with a nitrogen design limit; for facilities without a 

design limit, constant nitrogen values were determined based 

on population (U.S. Census Bureau, 2000); and for facilities 

with controlled discharge, a combination of methods was used, 

allowing for nitrogen accumulation until time of discharge. 

Potential evapotranspiration (PET), surface runoff, and 

routing methods, as well as land-management operations, must 

be selected in the model. In this case the Hargreaves method 

for estimating PET, which only requires temperature data for 

input, was selected (Hargreaves and others, 2003). Two methods for estimating surface runoff are provided in SWAT and 

include the Green and Ampt (Green and Ampt, 1911) equation 

and the CN method. The CN method, which estimates surface 

runoff based on hydrologic soil group, land cover, and antecedent moisture condition, was selected. The variable-storage 

(Williams, 1969) and Muskingum method (McCarthy, 1938) 

are available for simulating channel routing. Both methods 

are variations of the kinematic wave model. The Muskingum 

method was selected because it improved the timing of peak 

flows relative to the variable-storage routing method. 

For simplification, a corn-soybean rotation was implemented basinwide, and includes fertilizer and manure applications (table 3). The ISU Extension Office recommends 

an application rate of 100–150 pounds per acre (lbs/ac) 

(112–168 kilograms per hectare (kg/ha)) of nitrogen for corn 

following soybeans (J. Faucett, ISU Extension Office, written 

and oral commun., 2011). Available data (National Agricultural Statistics Service, Census of Agriculture, 2007a, 2007b) 

suggests that the number of acres treated with fertilizer, as 

well as the number of cropland acres harvested, increased 

approximately 20 percent from 2002 to 2007 for those counties that constitute the Cedar River Basin. The 2008 CDL was 

used for representing land cover in this model. Land cover, 

and thus number of acres of land-cover type receiving fertilizer, is static, therefore the rates of fertilizer application were 

reduced by 20 percent for the calibration period (2000–04) to 

reflect the smaller number of cropland acres in 2002 relative 

to 2007. Depending on location within the basin, a fertilizer 

rate of 71 to 125 lbs/ac (80 to 140 kg/ha) of monoammonium 

phosphate (11-52-00: nitrogen-phosphorus-potassium) was 

applied before corn planting, and a fertilizer rate of 80 to 

Table 3. Management operation schedule for corn and 

soybeans for the Cedar River Basin model, Iowa. 

[11-52-00, monoammonium phosphate]

Crop Management operation

Date (for each 

year of 

simulation)

Corn Manure application April 1

Tillage April 18

Fertilizer application, 11-52-00 April 20

Plant/begin growing season April 25

Harvest and kill October 15

Soybean Plant/begin growing season May 5

Harvest and kill October 15

Manure application October 20

Fertilizer application, anhydrous 

ammonia

November 1
Methods 13

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93°

94°

92°

91°

91°

44°

43°

42°

STEELE

COUNTY

DODGE

COUNTY

MITCHELL

COUNTY

WORTH

COUNTY

TAMA

COUNTY

WINNEBAGO

COUNTY

BUTLER

COUNTY

FRANKLIN

COUNTY

BENTON

COUNTY

MOWER COUNTY

WRIGHT

COUNTY

HANCOCK

COUNTY

BREMER

COUNTY

MARSHALL

COUNTY

IOWA COUNTY

FREEBORN COUNTY

CERRO

GORDO

COUNTY

FLOYD

COUNTY

BUCHANAN

COUNTY

BLACK HAWK

COUNTY

JONES

COUNTY

FERIBAULT

COUNTY

CHICKASAW

COUNTY

HOWARD

COUNTY

GRUNDY

COUNTY

HARDIN

COUNTY

LINN

COUNTY

MUSCATINE

COUNTY

SCOTT COUNTY

LOUISA

COUNTY

CEDAR

COUNTY

JOHNSON

COUNTY

MINNESOTA

IOWA

IOWA

ILLINOIS

Cedar River

elttiL

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

Cedar RiverCedar River

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

elttiL

EXPLANATION

Cedar River Basin boundary

High

Infiltration rate

Moderate

Slow

Very slow

Soils data from the U.S. Department of AgricultureNatural Resources Conservation Service, Soil

Survey Geographic (SSURGO) Database, 2009

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Base from U.S. Geological Survey digital data, variously 

dated, various scales

Universal Transverse Mercator projection, Zone 15

North Amercian Datum of 1983

Figure 6. Relative soil infiltration rates in the Cedar River Basin, Iowa. 
14 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

161 lb/ac (90 to 180 kg/ha) of anhydrous ammonia was 

applied after soybean harvest. 

Manure land application also was simulated for corn for 

spring and fall and these simulated amounts were estimated 

based on the livestock numbers reported in the 2007 Census of 

Agriculture (Ag Census) (National Agricultural Statistics Service, Census of Agriculture, 2007c-g) for the Minnesota part 

of the basin, and on IDNR GIS coverages of feedlots for the 

Iowa part of the basin (Iowa Department of Natural Resources, 

2006b, 2006c). Manure rates also were decreased 20 percent 

for the calibration period (2000–04); a comparison of the 

livestock inventory from the 2002 and 2007 Ag Census indicates that livestock in the basin increased by approximately 

20 percent from 2002 to 2007 (National Agricultural Statistics Service, Census of Agriculture, 2007c-g). Following the 

guidelines used in the Cedar River Watershed TMDL for E. 

coli report (U.S. Environmental Protection Agency, 2010), the 

livestock population for Minnesota subbasins was estimated 

by reducing the reported number of livestock per county (beef 

and dairy cattle, hogs, and sheep) by the proportion of subbasin within that county. The amount of manure distributed 

by way of grazing (beef and sheep only) also was reduced. 

Manure production rates by animal listed in the SWAT Input/

Output File documentation, Version 2009 (Arnold and others, 

2010), as well as area of land grazed, were then used to calculate subbasin manure input per acre from grazing. 

To simulate tile flow, values must be set for the depth 

to subsurface drains (DDRAIN), the time to drain the soil to 

field capacity (TDRAIN), and the time between the transfer 

of water from the soil to the drain tile, and then from the 

drain tile to the reach (GDRAIN). In addition, initiation of 

tile flow requires that a depth to impervious layer (DEP_IMP) 

be set at approximately the same depth as the tile drain. A 

GIS coverage representing soils that require tile drainage was 

obtained from the IDNR (fig. 7) (Iowa Department of Natural 

Resources, 2008b), and was overlain with the soils layer in 

SWAT to determine the soil types likely to be drained. Tile 

data were not available for the Minnesota part of the basin but 

the soils likely to be tiled as determined from the Iowa data 

were considered basinwide. Tile drainage was implemented 

for those HRUs characterized by soils likely to be drained, 

corn or soybean land cover, and low slopes (0–2 percent). 

Streamflow data were obtained for each of the streamflow-gaging stations used in model calibration and validation 

from the National Water Information System (NWIS) Web 

service (table 1; U.S. Geological Survey, 2011). Nitrate concentration data and corresponding streamflow were obtained 

from three IDNR STORET/WQX (Iowa Department of Natural Resources, 2010b) stations for nitrate load calibration and 

validation. 

Subbasin Delineation

Basin delineation is the first step in the model setup, 

and begins by using a Digital Elevation Model (DEM) and 

hydrography dataset to partition the basin into subbasins. A 

threshold value can be set by the user to control the density 

of the stream network and thus the resulting number of subbasins. In this case, the threshold was set so that the resulting 

subbasin boundaries would coincide with Hydrologic Unit 

Code (HUC) 12 boundaries. Some minor discrepancies occur 

because not all streamflow-gaging stations coincide with 

HUC 12 basin outlets. All streamflow-gaging stations used for 

calibration must be included as basin outlets so that simulated 

model output is provided at these locations for comparison to 

measured data. Sensitivities can be specified for land cover, 

soil, and slope to determine HRU distribution; in this case the 

sensitivity was set to 5 percent for each. Before HRU definition, slope was separated into four categories including less 

than 2 percent, 2 percent to 4 percent, greater than 4 percent to 

9 percent, and greater than 9 percent (fig. 8). The final delineation resulted in a total of 14,234 HRUs and 227 subbasins 

(fig. 9); however, outlet 226 represents the farthest downstream streamflow-gaging station from the basin, USGS 

streamflow-gaging station Cedar River near Conesville, IA 

(table 1), and was thus selected as the whole basin outlet. 

Model Calibration 

Statistical Evaluation of Model Performance 

The Nash-Sutcliffe coefficient of model efficiency (ENS) 

(Nash and Sutcliffe, 1970), coefficient of determination (R2), 

and percent bias (PBIAS) were selected for quantitatively 

evaluating model performance. The ENS is a measure of how 

well the simulated values agree with the measured values, 

and can range between negative infinity and 1. The closer the 

value is to one the better the predictive power of the model. 

The ENS model performance ratings proposed for all constituents by Moriasi and others (2007) was used to evaluate model 

calibration and validation and are as follows: “very good” 

if the monthly ENS is greater than or equal to 0.75, “good” if 

the monthly ENS is greater than or equal to 0.65 but less than 

0.75, “satisfactory” if the monthly ENS is greater or equal to 

0.5 but less than 0.65, and “unsatisfactory” if the monthly ENS

is less than 0.5. Moriasi and others (2007) propose appropriate adjustments of these ratings for daily and annual time step 

evaluations, respectively, and note that shorter time steps (for 

example, daily) typically produce poorer results than longer 

time steps (for example, annual). 

The R2 value is the proportion of the variability in the 

measured data that is explained by the simulated data, and 

is a measure of the strength of the linear relation between 

predicted and measured values. It can range between 0 and 1, 

and the closer the value is to 1 the better the linear correlation 

between measured and simulated values (Kalin and Hantush, 

2006). Gassman and others (2007) considered an R2 value of 

greater than 0.5 as satisfactory when comparing across multiple SWAT studies. 

The PBIAS is a measure of the average tendency of overpredictions and underpredictions of the simulated data for the 

time period being evaluated (Bumgarner and Thompson, 2012; 
Methods 15

Soils requiring tile drainage

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93°

94°

92°

91°

91°

44°

43°

42°

STEELE

COUNTY

DODGE

COUNTY

MITCHELL

COUNTY

WORTH

COUNTY

TAMA

COUNTY

WINNEBAGO

COUNTY

BUTLER

COUNTY

FRANKLIN

COUNTY

BENTON

COUNTY

MOWER COUNTY

WRIGHT

COUNTY

HANCOCK

COUNTY

BREMER

COUNTY

MARSHALL

COUNTY

IOWA COUNTY

FREEBORN COUNTY

CERRO

GORDO

COUNTY

FLOYD

COUNTY

BUCHANAN

COUNTY

BLACK HAWK

COUNTY

JONES

COUNTY

FERIBAULT

COUNTY

CHICKASAW

COUNTY

HOWARD

COUNTY

GRUNDY

COUNTY

HARDIN

COUNTY

LINN

COUNTY

MUSCATINE

COUNTY

SCOTT COUNTY

LOUISA

COUNTY

CEDAR

COUNTY

JOHNSON

COUNTY

EXPLANATION

Cedar River Basin boundary

MINNESOTA

IOWA

Cedar RiverCedar River

elttiL 

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

IOWA

ILLINOIS

Soils data from Iowa Department of Natural Resources,

Geographic Information Systems Library, Soils Requiring

Tile Drainage for Full Productivity, 2008

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Base from U.S. Geological Survey digital data, variously 

dated, various scales

Universal Transverse Mercator projection, Zone 15

North Amercian Datum of 1983

Figure 7. Soil types likely to be drained in the Iowa part of the Cedar River Basin, Iowa. 
16 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

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93°

94°

92°

91°

91°

44°

43°

42°

STEELE

COUNTY

DODGE

COUNTY

MITCHELL

COUNTY

WORTH

COUNTY

TAMA

COUNTY

WINNEBAGO

COUNTY

BUTLER

COUNTY

FRANKLIN

COUNTY

BENTON

COUNTY

MOWER COUNTY

WRIGHT

COUNTY

HANCOCK

COUNTY

BREMER

COUNTY

MARSHALL

COUNTY

IOWA COUNTY

FREEBORN COUNTY

CERRO

GORDO

COUNTY

FLOYD

COUNTY

BUCHANAN

COUNTY

BLACK HAWK

COUNTY

JONES

COUNTY

FERIBAULT

COUNTY

CHICKASAW

COUNTY

HOWARD

COUNTY

GRUNDY

COUNTY

HARDIN

COUNTY

LINN

COUNTY

MUSCATINE

COUNTY

SCOTT COUNTY

LOUISA

COUNTY

CEDAR

COUNTY

JOHNSON

COUNTY

MINNESOTA

IOWA

IOWA

ILLINOIS

Cedar River

elttiL

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

Cedar RiverCedar River

Cedar

River

WinnebagoWinnebago

River

West Fork Cedar River

River

Shell Rock

B

Creek eaver

Black Hawk

Creek

Wolf Creek

Iowa River

elttiL

EXPLANATION

0 to 2

Slope category, in percent

Greater than 2 to 4

Greater than 4 to 9

Greater than 9

Cedar River Basin boundary

Slope data modifed from U.S. Geological Survey

National Elevation Dataset, 2009

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Base from U.S. Geological Survey digital data, variously 

dated, various scales

Universal Transverse Mercator projection, Zone 15

North Amercian Datum of 1983

Figure 8. Percent slope for the Cedar River Basin model, Iowa.
Methods 17

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EXPLANATION

! ! ! ! Cedar River Basin boundary

Model stream reach

Model subbasin and number

93°

92°

91°

43°

42°

199

0 15 30 45 60 MILES

0 15 30 45 60 KILOMETERS

Figure 9. Subbasin delineation for the Cedar River Basin model, Iowa.
18 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Moriasi and others, 2007; Gupta and others, 1999). A PBIAS 

value of 0.0 indicates ideal performance, while positive values 

indicate underestimation bias and negative values indicate 

overestimation bias (Moriasi and others, 2007). Model performance for streamflow is considered “very good” if the PBIAS 

is between 0 and plus or minus (+/-) 10 percent, “good” if the 

PBIAS is between +/- 10 and +/- 15 percent, “satisfactory” if 

the PBIAS is between +/- 15 and +/- 25 percent, and “unsatisfactory” if the PBIAS is +/-25 percent or greater (Moriasi and 

others, 2007). Model performance for nitrogen is considered 

very good if the PBIAS is between 0 and +/-25 percent, good 

if the PBIAS is between +/-25 and +/-40 percent, satisfactory 

if the PBIAS is between +/- 40 and +/-70 percent, and unsatisfactory if the PBIAS is +/-70 percent or greater (Moriasi and 

others, 2007). 

The variables ENS, R2, and PBIAS are defined as follows: 

 (1)

 (2)

 (3)

where

qobs,i is the measured streamflow at the ith time 

step; 

qsim,i is the simulated streamflow at the ith time 

step;

qobs is the measured mean streamflow for the time 

period; 

qsim is the simulated mean streamflow for the time 

period; and

N is the number of observations. 

Hydrology Calibration 

A 5-year and 6-year period that included wet and dry 

years were selected for model calibration (January 1, 2000, 

to December 31, 2004) and validation (January 1, 2005, to 

December, 31, 2010), respectively. The initial group of calibration parameters was selected based on previous published 

studies that assessed the sensitivity of parameters for Iowa, 

as well as other Midwestern agricultural basins. Calibration 

was completed by manually adjusting parameter values within 

their acceptable ranges (Arnold and others, 2010) to match 

simulated to measured streamflow at each of the 12 USGS 

streamflow-gaging stations listed in table 1 and shown in 

figure 2. Calibration was first completed for average annual 

conditions, followed by average monthly, and finally daily 

conditions, starting with the farthest upstream streamflow-gaging station for each tributary and moving downstream to the 

next consecutive streamflow-gaging station. Performance was 

evaluated by determining the ENS, R2

 of the linear regression, 

and the PBIAS for each streamflow-gaging station. A total of 

16 streamflow parameters were designated as sensitive and 

thus manually adjusted for calibration. The selected hydrology 

parameters and parameter descriptions are listed in table 4. 

The final hydrology calibration values are listed in table 5. 

Nitrate Load Calibration 

Nitrate concentration and corresponding streamflow for 

the calibration (2000–04) and validation period (2005–10) 

were collected from three Iowa STORET/WQX Water Quality 

ENS = 1 – [∑N

i =1 

(qobs,i – qsim,i)

2

]

[∑N

i =1 

(qobs,i – qobs)

2

]

R2 = [∑N

i = 1 

(qobs,i – qobs)2][∑N

i =1 

(qsim,i – qsim)2]

[∑N

i =1 

(qobs,i – qobs)(qsim,i – qsim)]

2

PBIAS= *100

∑N

i =1 

(qobs,i – qsim,i)

∑N

i = 1 

qobs,i

Table 4. Soil and water assessment tool (SWAT) hydrology 

calibration parameters and parameter descriptions for the 

Cedar River Basin model, Iowa. 

[SCS, Soil conservation service; mm, millimeters; mm water/mm soil, millimeters of water per millimeters of soil; ET, actual evapotranspiration]

SWAT calibration 

parameter (units)

Parameter description

CN2 (dimensionless) SCS runoff curve number for moisture 

condition II.

SOL_AWC (mm 

water/mm soil)

Available water capacity

ESCO Soil evaporation compensation factor; accounts for the effect of cracking, crusting, and capillary action by adjusting the 

depth distribution used to the meet the 

soil evaporative demand.

REVAPMN (mm) Amount of water required in the shallow aquifer for percolation to the deep 

aquifer or movement of water to the 

unsaturated zone to occur.

GWQMN (mm) Threshold depth of water in the shallow 

aquifer required for return flow to occur. 

GW_REVAP Regulates movement of water between the 

shallow aquifer and root zone. 

ALPHA_BF (days) Base-flow recession constant. 

CNCOEF Plant ET curve number coefficient.

OV_N (days) Manning’s “n” for overland flow.

CH_N1 Manning’s “n” for tributary channels.

CH_N2 Manning’s “n” for the main channel.

SURLAG (days) Surface lag coefficient. 

GW_DELAY (days) Delay time for aquifer recharge.

DDRAIN (mm) Depth to subsurface drains.

TDRAIN (hours) Time to drain the soil to field capacity. 

GDRAIN (hours) Time between transfer of water from the 

soil to drain tile and drain tile to the 

reach.

DEP_IMP (mm) Depth to an impervious layer in the soil 

profile; necessary for tile flow.
Methods 19

Table 5. Soil and Water Assessment Tool final hydrology calibration values for the Cedar River Basin model, Iowa. [MN, Minnesota; IA, Iowa; CN2, Moisture condition II curve number; SOL_AWC, Soil available water capacity; ESCO, Soil evaporation compensation factor; REVAPMN, Threshold depth of water in the shallow aquifer for “revap” to occur; GWQMN, Threshold water level in shallow aquifer required for return flow to occur; GW_REVAP, Revap coefficient; ALPHA_BF, Base-flow recession constant; CH_N1, Manning’s “n” value for the tributary channels; CH_N2, Manning’s “n” value for the main channel; OV_N, Manning’s “n” value for overland flow; SURLAG, Surface runoff lag time; GW_DELAY, Groundwater delay; DDRAIN, Depth to subsurface drain; TDRAIN, Time to drain soil to field capacity; GDRAIN, Drain tile lag time; DEP_IMP, Depth to impervious layer in soil profile; ICN, Daily curve number calculation method; CNCOEF, Plant ET curve number coefficient; ET, actual evapotranspiration]

Streamflow-gaging station Calibrated parameter value CN2 SOL_AWC ESCO REVAPMN GWQMN GW_REVAP ALPHA_BF CH_N1 CH_N2

Cedar River near Austin, Minnesota -8 - 0.8 1.02 0 0.02 0.1 0.04 0.04

Winnebago River at Mason City, Iowa -8 +0.01 0.75 0.98 0.1 0.02 0.1 0.04 0.04

Little Cedar River near Ionia, Iowa -6 - 0.8 0.87 0.1 0.02 0.1 0.025 0.025

Shell Rock River at Shell Rock, Iowa -8 - 0.95 0.93 0.1 0.02 0.1 0.025 0.025

West Fork Cedar River at Finchford, 

Iowa

-8 - 0.85 1 0 0.02 0.1 0.04 0.04

Cedar River at Janesville, Iowa -8 - 0.80 1 0 0.02 0.1 0.025 0.025

Beaver Creek at New Hartford, Iowa -8 +0.02 0.85 0.97 0 0.02 0.1 0.045 0.045

Cedar River at Waterloo, Iowa -6 - 0.85 1.35 0 0.02 0.1 0.025 0.025

Black Hawk Creek at Hudson, Iowa -6 +0.02 0.85 1 0 0.02 0.5 0.025 0.025

Wolf Creek near Dysart, Iowa -2 - 0.85 1 0 0.02 0.1 0.025 0.025

Cedar River at Cedar Rapids, Iowa -6 - 0.85 1.35 0 0.02 0.1 0.025 0.025

Cedar River near Conesville, Iowa -4 - 0.80 1 0 0.02 0.1 0.03 0.03

Streamflow-gaging station Calibrated parameter value OV_N SURLAG GW_DELAY DDRAIN TDRAIN GDRAIN DEP_IMP ICN CNCOEF

Cedar River near Austin, Minnesota 0.12 2 62 1,200 36 72 1,200 1 0.3

Winnebago River at Mason City, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3

Little Cedar River near Ionia, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3

Shell Rock River at Shell Rock, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3

West Fork Cedar River at Finchford, 

Iowa

0.12 2 62 1,200 36 96 1,200 1 0.3

Cedar River at Janesville, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3

Beaver Creek at New Hartford, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3

Cedar River at Waterloo, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3

Black Hawk Creek at Hudson, Iowa 0.12 2 62 1,200 36 96 1,200 1 0.3

Wolf Creek near Dysart, Iowa 0.12 2 62 1,200 36 96 1,200 1 0.3

Cedar River at Cedar Rapids, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3

Cedar River near Conesville, Iowa 0.12 2 62 1,200 36 72 1,200 1 0.3
20 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Database stations (Iowa Department of Natural Resources, 

2010b), that correspond to three USGS streamflow-gaging 

stations, listed in table 1 and shown in figure 2. These data are 

a compilation of single grab samples collected on a monthly 

basis. Continuous average monthly and yearly nitrate loads 

were estimated for the period of record from the grab samples 

using the USGS Load Estimator (LOADEST) regression 

model (Runkel and others, 2004). Provided a time series of 

discrete measured streamflow and constituent concentrations, 

LOADEST can be used to develop a regression model for 

estimating constituent loads in streams and rivers (Runkel 

and others, 2004). There are three statistical methods that 

the model uses to estimate constituent loads. In this case, the 

Adjusted Maximum Likelihood Estimation (AMLE) method 

was used. The form of the regression model used to generate continuous loadings is user-selected and the option for 

allowing LOADEST to select the best regression model was 

selected in this case (table 6). There were no sample values 

below analytical detection limits. The resulting estimated 

time-series data were then used in place of measured data for 

completing the annual and monthly nitrate calibration and 

validation. The LOADEST statistical modeling results are 

listed in table 6. 

Nitrate load calibration was completed by manually 

adjusting parameter values within their acceptable ranges to 

match simulated nitrate loads to LOADEST nitrate loads. 

Calibration was first completed for average annual conditions 

followed by average monthly conditions. Performance was 

evaluated by determining the ENS and R2 values for each Iowa 

STORET/WQX Water Quality Database station. A total of 

four nutrient parameters were manually adjusted for calibration. The selected parameters, parameter descriptions, 

and final nitrate calibration parameter values are listed in 

table 7. Management operations also were considered calibration parameters (table 3). 

Model Limitations

Measurement errors that can affect model performance 

include resolution of land cover, assumed static land cover 

through the simulation period, resolution and availability of 

land management operation data and application at the subbasin to basinwide level, availability of nitrate data, modelestimated average measured yearly and monthly nitrate values, 

and distribution of point measurements of precipitation and 

temperature across the basin. 

The CDL was selected to represent land cover because 

of the great detail that is provided for the land cover-classes, 

specifically agricultural crops. However, the resolution of the 

CDL is coarser (57 meters (m)) relative to other land-cover 

layers that could have been used. This could cause overestimation or underestimation in certain land-cover types, thus 

affecting rainfall-runoff calculations. 

Land cover was considered static through time and thus 

changes were not accounted for, including years in which 

management operations would have been altered because of 

short-term events such as flooding. For example, the timing 

Table 6. LOADEST statistical modeling results for each streamflow-gaging station for the Cedar River Basin model, Iowa, 2000–10. 

[N., number; obs., observations; ln, natural logarithm; L, daily load in kilograms per day; Q, centered mean daily streamflow in cubic feet per second; SS, 

seasonality parameter (2π*decimal years (centered)); Ave., average; m., monthly; Std., standard; dev., deviation; a., annual; Est., estimated; res., residual; var., 

variance; R2, coefficient of determination; %, percent]

Streamflow-gaging 

station

N. 

obs. Regression model

Ave. m. 

load 

(tons)

Std. dev. 

(tons)

Ave. a. 

load 

(tons)

Std. dev. 

(tons)

Est. res. 

var.

R2

 (%)

Shell Rock River at 

Shell Rock, Iowa

126 ln(L) = 9.97 + 1.36*lnQ – 0.140*lnQ2

 + 

0.284*sin(SS) + 0.263*cos(SS)

848 1,112 9,707 3,915 0.1383 94

Cedar River at Janesville, Iowa110 ln(L) = 10.3 + 1.37*lnQ – 0.163*lnQ2

 + 

0.176*sin(SS) + 0.281*cos(SS)

945 1,195 10,735 4,543 0.1379 93

Cedar River near 

Conesville, Iowa

117 ln(L) = 11.6 + 1.71*lnQ – 0.320*lnQ2

 + 

0.318*sin(SS) + 0.533*cos(SS)

5,036 6,352 60,436 37,841 0.4398 82

Table 7. Soil and water assessment tool (SWAT) nitrate 

calibration parameters, parameter descriptions, and final 

calibration values for the Cedar River Basin model, Iowa. 

[°C, degrees Celsius; day-1, per day; NH4, ammonium; NO2, nitrite; 

N, nitrogen; P, phosphorus]

SWAT 

calibration 

parameter

Parameter description

Final 

calibrated 

value

CDN Denitrification exponential rate coefficient; controls rate of denitrification0.6

RS4 Rate coefficient for organic N settling 

in the reach at 20 oC (day-1)

0.1

BC1 Rate constant for biological oxidation 

of NH4

 to NO2 in the reach at 20 oC 

in well-aerated conditions (day-1)

0.5

CMN Rate factor for humus mineralization of 

active organic nutrients (N and P) 

0.0001
Hydrology and Water Quality Simulation 21

of the 2008 floods allowed for some crops to actually be 

replanted later in the season. 

In addition to fertilizer and manure data being compiled 

and published every 5 years, the amount of estimated corn 

and soybean acres affects the estimated manure application 

rates. In an attempt to compensate for manure application rate 

increases through time, as suggested by NASS data, higher 

rates were applied during the validation period relative to the 

calibration period. Manure and fertilizer rates also can change 

from year to year depending on a number of factors and this is 

not captured in 5-year compilations. Other operations such as 

planting, tillage, and harvest may be altered from field to field 

as well as from year to year. However, because of the lack of 

this information as well as the time requirement for implementing management operations at a finer resolution than at 

the subbasin, and sometimes basinwide, level for the Cedar 

River Basin, generalized management operations that were 

uniform from year to year had to be applied. 

Monthly grab-sample data were available for only three 

nutrient stations, limiting the data available for calibration. 

In addition, the monthly data were used to estimate average 

monthly and yearly values. Measurement errors could occur 

in the grab-sample results that were used to estimate monthly 

and annual measured loads. Additional errors are introduced in 

the model (LOADEST) used to make these average measured 

estimates for use in calibration. 

There are also errors inherent to the model, such as systematic errors that result simply from the limitations of model 

parameters and equations to replicate the processes occurring 

in the basin. In addition, for SWAT specifically, precipitation 

and temperature point data are distributed in space across the 

basin, with subbasins receiving point values of the closest 

climate station, instead of a gradient being applied across the 

basin based on the available point values. Isolated precipitation events can cause over estimation of rainfall, while events 

occurring between streamflow-gaging stations might cause the 

model to under-predict rainfall amounts, affecting the amount 

of rainfall-produced-runoff from an HRU.

Hydrology and Water Quality 

Simulation

Hydrology Calibration and Validation Results

Daily, monthly, and annual ENS, R2, and PBIAS values, 

along with descriptive statistics, were determined for 

hydrology calibration, January 1, 2000, to December 31, 

2004 (fig. 10, table 8), and validation, January, 1, 2005 to 

December 31, 2010 (fig. 11, table 9), for all 12 USGS streamflow-gaging stations ("streamflow-gaging station" will be 

referred to as "station" for the entire results section); please 

refer to table 1 and figure 2 for cross-referencing station 

names and locations. Results indicate that SWAT is capable of 

predicting hydrology; calibration ENS and R2

 values are greater 

than 0.5 for all locations and time steps with the exception of 

the Cedar River near Austin, MN, station with a daily ENS of 

0.44. The monthly calibration and validation ENS for the Cedar 

River at Austin, MN, station indicates good model performance whereas monthly calibration and validation ENS values 

indicate very good model performance for all other locations. 

Monthly PBIAS results indicate satisfactory to very good 

model performance. 

Annual calibration ENS values range from 0.56 for the 

Cedar River near Austin, MN, station to 0.97 for the Winnebago River at Mason City, IA, station while annual calibration R2

 values range from 0.65 for the Cedar River near 

Austin, MN, station to 0.99 for the West Fork Cedar River at 

Finchford, IA, station and the Cedar River near Conseville, 

IA, station. Annual calibration PBIAS ranges from -19 percent 

for the Shell Rock River at Shell Rock, IA, station to 10 percent for the Black Hawk Creek at Hudson, IA, station. 

 Monthly calibration ENS values range from 0.72 for the 

Cedar River near Austin, MN, station to 0.93 for the Cedar 

River near Conesville, IA, station while monthly calibration 

R2 values range from 0.74 for the Cedar River near Austin, 

MN, station to 0.94 for the Cedar River at Waterloo, IA, station and the Cedar River at Cedar Rapids, IA, station. Monthly 

calibration PBIAS ranges from -16 percent for the Shell Rock 

River at Shell Rock, IA, station to 10 percent for the Black 

Hawk Creek at Hudson, IA, station. 

Finally, daily calibration ENS values range from 0.44 for 

the Cedar River near Austin, MN, station to 0.83 for the Cedar 

River near Conesville, IA, station while daily calibration R2

values range from 0.55 for the Cedar River near Austin, MN, 

station to 0.87 for the Cedar River at Cedar Rapids, IA, station. Daily calibration PBIAS ranges from -19 percent for the 

Shell Rock River at Shell Rock, IA, station to 10 percent for 

the Black Hawk Creek at Hudson, IA, station. 

Although monthly validation results indicate good to very 

good model performance the annual validation ENS dropped 

below zero for the Shell Rock River at Shell Rock, IA, station 

(-0.22), and below 0.5 for the Winnebago River at Mason City, 

IA, station. Outside of these exceptions, annual validation ENS

values range from 0.59 for the Little Cedar River near Ionia, 

IA, station to 0.95 for the West Fork Cedar River at Finchford, 

IA, station. Annual validation R2 values range from 0.36 for 

the Winnebago River at Mason City, IA, station to 0.92 for 

the Black Hawk Creek at Hudson, IA, station. Annual validation PBIAS ranges from -16 percent for the Shell Rock River 

at Shell Rock, IA, station to 15 percent for the Black Hawk 

Creek at Hudson, IA, station. 

Monthly validation ENS values range from 0.69 for the 

Cedar River near Austin, MN, station to 0.91 for the Little 

Cedar River near Ionia, IA, station while monthly validation 

R2 values range from 0.74 for the Wolf Creek near Dysart, IA, 

station to 0.92 for the Little Cedar River near Ionia, IA, station. Monthly validation PBIAS ranges from -16 percent for 

the Shell Rock River at Shell Rock, IA, station to 15 percent 

for the Black Hawk Creek at Hudson, IA, station. 
22 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Table 8. Hydrology calibration (January 1, 2000, to December 31, 2004) results for each streamflow-gaging station for the Cedar River 

Basin model, Iowa.

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Cedar River near Austin, Minnesota

Daily 0.44 0.55 4% 43 15,000 325 122 4 16,951 313 108

Monthly 0.72 0.74 4% 48 2,328 325 142 13 2,162 310 142

Annual 0.56 0.65 4% 166 457 325 393 188 482 313 220

Winnebago River at Mason City, Iowa

Daily 0.69 0.75 -3% 17 7,550 359 127 1 7,098 370 142

Monthly 0.88 0.89 -3% 28 2,510 359 151 14 2,247 366 146

Annual 0.97 0.98 -3% 237 555 359 249 232 546 370 299

Little Cedar River near Ionia, Iowa

Daily 0.66 0.68 -16% 12 7,530 197 61 4 4,520 228 87

Monthly 0.88 0.89 -15% 18 1,636 196 70 7 1,241 226 122

Annual 0.83 0.96 -16% 84 303 197 202 137 338 228 217

Shell Rock River at Shell Rock, Iowa

Daily 0.65 0.78 -19% 142 23,900 1,175 475 66 24,226 1,405 650

Monthly 0.89 0.90 -16% 174 8,236 1,173 549 94 7,037 1,387 825

Annual 0.68 0.92 -19% 657 1,774 1,174 901 955 2,063 1,404 1,138

West Fork Cedar River at Finchford, Iowa

Daily 0.80 0.81 -8% 32 11,300 539 210 23 6,992 583 268

Monthly 0.92 0.92 -8% 64 2,959 537 219 47 3,051 570 305

Annual 0.93 0.99 -8% 381 939 539 407 446 927 583 468

Cedar River at Janesville, Iowa

Daily 0.67 0.76 -6% 183 20,900 1,173 498 27 30,053 1,242 477

Monthly 0.89 0.90 -5% 219 8,056 1,172 542 45 7,081 1,235 602

Annual 0.91 0.93 -6% 577 1,698 1,173 1,202 774 1,862 1,242 1,089

Beaver Creek at New Hartford, Iowa

Daily 0.70 0.71 -9% 9 4,780 191 75 24 2,896 208 111

Monthly 0.83 0.84 -9% 21 920 190 81 34 698 201 131

Annual 0.74 0.82 -9% 120 260 191 179 160 301 208 167

Cedar River at Waterloo, Iowa

Daily 0.75 0.85 -7% 340 57,100 3,444 1,760 180 54,738 3,704 1,769

Monthly 0.92 0.94 -7% 628 19,412 3,437 1,863 269 18,414 3,649 2,141

Annual 0.93 0.98 -7% 2,175 4,837 3,443 2,924 2,578 5,086 3,703 3,225

Black Hawk Creek at Hudson, Iowa1

Daily 0.66 0.67 10% 6 5,450 125 50 3 1,793 113 37

Monthly 0.92 0.86 10% 14 793 124 57 12 489 105 63

Annual 0.84 0.97 10% 83 191 132 122 54 187 120 119
Hydrology and Water Quality Simulation 23

Finally, daily validation ENS values range from 0.49 for 

the Cedar River near Austin, MN, station to 0.77 for the Cedar 

River at Waterloo, IA, station and the Cedar River at Cedar 

Rapids, IA, station while daily validation R2 values range 

from 0.59 for the Cedar River near Austin, MN, station to 0.84 

for the Cedar River at Waterloo, IA, station. Daily validation PBIAS ranges from -16 percent for the Shell Rock River 

at Shell Rock, IA, station to 14 percent for the Black Hawk 

Creek at Hudson, IA, station. 

There were decreases and increases in the ENS and R2 

values for the validation period relative to calibration. The 

ENS values for all time steps for calibration and validation for 

the model outlet, the Cedar River near Conesville, IA, station 

ranged from 0.72 to 0.94, while R2 values ranged from 0.79 to 

0.99. The model performance based on the statistical measures 

is good to very good with the noted exceptions. 

Nitrate Calibration and Validation Results 

The annual and monthly ENS, R2, and PBIAS values 

were determined for nitrate calibration and validation and are 

listed in table 10. The calibration period resulted in ENS and R2

values greater than 0.6 for all time steps at all three locations 

with the exception of the monthly calibration ENS for the Cedar 

River at Janesville, IA, station (0.28). Annual calibration ENS

values range from 0.61 for the Cedar River at Janesville, IA, 

station to 0.86 for the Shell Rock River at Shell Rock, IA, station while annual calibration R2

 values range from 0.65 to 0.88 

for the same locations, respectively. Annual calibration PBIAS 

ranges from 4 percent for the Cedar River near Conesville, 

IA, station to 7 percent for the Cedar River at Janesville, IA, 

station. 

Monthly calibration ENS values for the Shell Rock River 

at Shell Rock, IA, station (0.65), and the Cedar River near 

Conesville, IA, station (0.82) indicate good to very good 

model performance. The monthly calibration R2 values for 

the Shell Rock River at Shell Rock, IA, station and the Cedar 

River near Conesville, IA, station were 0.77 and 0.81, respectively. Although the monthly calibration ENS for the Cedar 

River at Janesville, IA, station indicates unsatisfactory model 

performance, the monthly R2

 value of 0.65 indicates satisfactory performance for this location. The monthly calibration 

PBIAS ranges from 4 percent for the Cedar River near Conesville, IA, station to 7 percent for the Cedar River at Janesville, 

IA, station, indicating very good performance. 

Annual and monthly ENS values for the validation period 

were all below zero, with the exception of the monthly validation ENS for the Shell Rock River at Shell Rock, IA, station 

(0.39) and the monthly validation ENS for the Cedar River at 

Janesville, IA, station (0.1) indicating that the measured mean 

is actually a better predictor than the model; the model cannot 

accurately simulate nitrate loads for the 2005–10 time period. 

Annual validation resulted in R2 values of 0.48, 0.27, and 0.25 

for the Shell Rock River at Shell Rock, IA, station, the Cedar 

River at Janesville, IA, station, and the Cedar River near 

Conesville, IA, station, respectively, while monthly validation 

Table 8. Hydrology calibration (January 1, 2000, to December 31, 2004) results for each streamflow-gaging station for the Cedar River 

Basin model, Iowa.—Continued

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Wolf Creek near Dysart, Iowa2

Daily 0.55 0.58 3% 7 8,360 123 40 0 1,977 120 49

Monthly 0.91 0.84 2% 13 975 126 44 7 525 118 75

Annual 0.83 0.74 -3% 54 214 125 117 52 187 130 141

Cedar River at Cedar Rapids, Iowa

Daily 0.82 0.87 -8% 326 61,800 4,200 2,240 275 54,385 4,565 2,391

Monthly 0.92 0.94 -8% 722 21,148 4,193 2,372 494 20,069 4,488 2,654

Annual 0.91 0.98 -9% 2,716 6,172 4,200 3,639 3,211 6,208 4,564 3,939

Cedar River near Conesville, Iowa

Daily 0.83 0.86 -7% 660 69,200 5,052 2,760 357 55,091 5,424 3,252

Monthly 0.93 0.93 -7% 1,029 22,207 5,045 2,839 667 21,365 5,336 3,392

Annual 0.94 0.99 -7% 3,568 7,092 5,052 4,249 3,811 7,318 5,424 4,504

1

Measured data was unavailable for 2000 and a part of 2001; calibration statistics are based on a total of 1,212 measured daily values. 

2

Measured data was unavailable for 2000 and a part of 2001; calibration statistics are based on a total of 1,326 measured daily values. 
24 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Table 9. Hydrology validation (January 1, 2005, to December 31, 2010) results for each streamflow-gaging station for the Cedar River 

Basin model, Iowa.

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Cedar River near Austin, Minnesota1

Daily 0.49 0.59 -4% 49 11,500 350 175 18 8,405 375 162

Monthly 0.69 0.80 -4% 58 1,606 349 227 35 2,322 376 239

Annual 0.71 0.74 -4% 222 462 349 346 287 515 375 360

Winnebago River at Mason City, Iowa

Daily 0.74 0.76 4% 27 10,400 464 241 25 8,899 467 243

Monthly 0.87 0.87 4% 63 2,795 464 315 47 2,388 466 297

Annual 0.23 0.36 4% 314 582 464 467 355 594 466 471

Little Cedar River near Ionia, Iowa

Daily 0.62 0.63 -14% 17 21,400 265 116 21 10,100 312 135

Monthly 0.91 0.92 -14% 26 2,551 265 174 32 2,110 312 204

Annual 0.59 0.82 -14% 183 396 265 251 216 429 312 289

Shell Rock River at Shell Rock, Iowa

Daily 0.62 0.75 -16% 247 46,400 1,539 831 130 34,326 1,833 950

Monthly 0.79 0.86 -16% 289 9,999 1,538 1,111 210 10,186 1,831 1,234

Annual -0.22 0.50 -16% 1,095 2,024 1,539 1,521 1,398 2,403 1,832 1,733

West Fork Cedar River at Finchford, Iowa

Daily 0.58 0.77 -7% 43 23,300 955 492 40 20,694 1,034 473

Monthly 0.79 0.84 -7% 64 5,315 954 570 61 5,946 1,032 746

Annual 0.95 0.75 -7% 528 1,279 955 1,057 683 1,327 1,034 1,069

Cedar River at Janesville, Iowa

Daily 0.72 0.77 -3% 281 51,400 1,579 840 100 31,254 1,677 759

Monthly 0.87 0.89 -3% 322 10,778 1,581 1,129 134 10,200 1,677 1,117

Annual 0.81 0.83 -3% 1,157 2,176 1,579 1,548 1,315 2,185 1,677 1,529

Beaver Creek at New Hartford, Iowa

Daily 0.66 0.69 6% 26 15,700 443 213 28 10,771 423 197

Monthly 0.84 0.85 6% 38 2,917 443 297 42 2,242 422 274

Annual 0.82 0.85 6% 183 635 443 508 218 610 422 437

Cedar River at Waterloo, Iowa

Daily 0.77 0.84 -1% 710 104,000 5,366 3,040 406 98,175 5,588 2,818

Monthly 0.87 0.88 -1% 38 2,917 443 297 42 2,242 422 274

Annual 0.76 0.77 -1% 3,432 7,351 5,365 5,492 3,957 7,235 5,587 5,327

Black Hawk Creek at Hudson, Iowa

Daily 0.58 0.68 14% 9 10,600 381 192 13 13,667 331 130

Monthly 0.79 0.81 15% 11 2,102 384 244 20 2,408 331 199

Annual 0.81 0.92 15% 138 597 385 456 110 532 331 377
Hydrology and Water Quality Simulation 25

resulted in R2 values of 0.67, 0.5, and 0.54 for the same locations, respectively. PBIAS results ranged from 46 percent for 

the Shell Rock River at Shell Rock, IA, station to 68 percent 

for the Cedar River near Conesville, IA, station for monthly 

and annual time steps. 

Nitrate loads substantially were underestimated for the 

validation period. There was a notable increase in measured 

data values basinwide from 2007 to 2010; however, this was 

not reflected in model results even though simulated fertilizer and manure rates were increased for the validation period 

relative to the calibration period. Heavy precipitation events 

during this period resulted in large simulated exports of 

nitrogen in the organic and ammonia forms, while nitrate loads 

substantially were underestimated. 

Alternative Hydrology Scenario Calibration and 

Validation

The Cedar River Basin is a densely gaged basin; 

12 USGS streamflow-gaging stations were used in this study 

for hydrology model calibration and validation purposes. Successful calibration can be more difficult for basins that are not 

as densely gaged, resulting in decreased agreement between 

simulated results and measured data. An alternative hydrology 

calibration scenario was run to represent the situation with 

regard to streamflow-gaging station density, and thus calibration points, for application to other Iowa basins. This was 

done by removing a subset of the streamflow-gaging stations 

that had been incorporated in the first calibration; locations 

removed include the Cedar River near Austin, MN, station, 

the Winnebago River at Mason City, IA, station, the Little 

Cedar River near Ionia, IA, station, the Beaver Creek at New 

Hartford, IA, station, the Wolf Creek near Dysart, IA, station, 

and the Black Hawk Creek at Hudson, IA, station. Removing 

these streamflow-gaging stations left only those streamflowgaging stations on the main stem of the Cedar River; if a basin 

has few streamflow-gaging stations they will more likely be 

Table 9. Hydrology validation (January 1, 2005, to December 31, 2010) results for each streamflow-gaging station for the Cedar River 

Basin model, Iowa.—Continued

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Wolf Creek near Dysart, Iowa

Daily 0.58 0.66 12% 13 9,400 362 182 11 10,877 323 130

Monthly 0.72 0.74 13% 21 2,001 362 239 17 2,194 322 203

Annual 0.82 0.90 12% 100 625 362 399 100 528 323 374

Cedar River at Cedar Rapids, Iowa

Daily 0.77 0.82 -3% 916 138,000 6,771 3,940 572 119,717 7,151 3,885

Monthly 0.86 0.87 -3% 1,506 46,453 6,765 5,190 926 41,168 7,141 5,270

Annual 0.84 0.86 -3% 3,801 10,139 6,770 7,016 4,710 9,722 7,150 7,230

Cedar River near Conesville, Iowa

Daily 0.72 0.79 2% 983 119,000 8,490 5,170 890 132,077 8,510 4,803

Monthly 0.85 0.86 2% 1,658 47,687 8,475 6,087 1,496 47,275 8,497 6,259

Annual 0.85 0.88 2% 4,327 12,935 8,488 9,145 5,128 11,867 8,508 9,099

1

Measured data is missing for December 10, 2009, to December 31, 2009; validation statistics are based on 2,147 measured daily values. 

 

Table 10. Nitrate load calibration (January 1, 2000, to 

December 31, 2004) and validation (January 1, 2005, to 

December 31, 2010) results for selected streamflow-gaging 

stations for the Cedar River Basin model, Iowa. 

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; %, percent]

Calibration Validation

ENS R2 PBIAS ENS R2 PBIAS

Shell Rock River at Shell Rock, Iowa

Monthly 0.65 0.77 5% 0.39 0.67 46%

Annual 0.86 0.88 5% -6.80 0.48 46%

Cedar River at Janesville, Iowa

Monthly 0.28 0.65 7% 0.10 0.50 60%

Annual 0.61 0.65 7% -6.35 0.27 60%

Cedar River near Conesville, Iowa

Monthly 0.82 0.81 4% -0.20 0.54 68%

Annual 0.76 0.78 6% -2.73 0.25 68%
26 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

0

500

2,5002,0001,5001,000

0

500

3,0002,5002,0001,5001,000

0

800600400200

1,8001,6001,4001,2001,000

0

9,0008,0007,0006,0005,0004,0003,0002,0001,000

0

900800700600500400300200100

0

1999 2000 2001 2002 2003 2004 2005

500

3,5003,0002,5002,0001,5001,000

Monthly mean streamflow, in cubic feet per second

0

9,0008,0007,0006,0005,0004,0003,0002,0001,000

0

800700600500400300200100

0

5,000

25,00020,00015,00010,000

0

800600400200

1,2001,000

1999 2000 2001 2002 2003 2004 2005

0

5,000

25,00020,00015,00010,000

1999 2000 2001 2002 2003 2004 2005

0

5,000

25,00020,00015,00010,000

1999 2001 2002 2003 2004 2005 2000

Year

Cedar River near Austin, Minnesota Winnebago River at Mason City, Iowa Little Cedar River near Ionia, Iowa Shell Rock River at Shell Rock, Iowa

West Fork Cedar River at Finchford, IowaBlack Hawk Creek at Hudson, Iowa

Cedar River at Janesville, Iowa Beaver Creek at New Hartford, Iowa Cedar River at Waterloo, Iowa

Wolf Creek near Dysart, Iowa Cedar River at Cedar Rapids, Iowa Cedar River near Conesville, Iowa

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

SimulatedMeasured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Figure 10. Calibration plots of measured and simulated monthly mean streamflow for each streamflow-gaging station in the Cedar River Basin model, Iowa.
Hydrology and Water Quality Simulation 27

0

800600400200

1,8001,6001,4001,2001,000

0

500

3,0002,5002,0001,5001,000

0

500

3,0002,5002,0001,5001,000

0

8,0006,0004,0002,000

12,00010,000

0

6,0005,0004,0003,0002,0001,000

Monthly mean streamflow, in cubic feet per second

0

8,0006,0004,0002,000

12,00010,000

0

500

3,5003,0002,5002,0001,5001,000

0

5,000

40,00035,00030,00025,00020,00015,00010,000

0

500

2,5002,0001,5001,000

0

500

2,5002,0001,5001,000

0

5,000

50,00045,00040,00035,00030,00025,00020,00015,00010,000

0

60,00050,00040,00030,00020,00010,000

2004 2005 2006 2007 2008 2009 2010 2011 2004

Year

2005 2006 2007 2008 2009 2010 2011 2004 2005 2006 2007 2008 2009 2010 2011 2004 2005 2006 2007 2008 2009 2010 2011

Cedar River near Austin, Minnesota Winnebago River at Mason City, Iowa Little Cedar River near Ionia, Iowa Shell Rock River at Shell Rock, Iowa

West Fork Cedar River at Finchford, IowaBlack Hawk Creek at Hudson, Iowa

Cedar River at Janesville, Iowa Beaver Creek at New Hartford, Iowa Cedar River at Waterloo, Iowa

Wolf Creek near Dysart, Iowa Cedar River at Cedar Rapids, Iowa Cedar River near Conesville, Iowa

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Measured

EXPLANATION

Simulated

Figure 11.

Validation plots of measured and simulated monthly mean streamflow for each streamflow-gaging station in the Cedar River Basin model, Iowa.
28 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

located on the main stem of the river rather than the smaller 

tributaries. The subbasins originally calibrated for hydrology 

based on the removed streamflow-gaging stations were instead 

calibrated based on the retained streamflow-gaging station 

locations farther downstream. Thus, subbasins originally 

calibrated on streamflow-gaging station data from the Cedar 

River near Austin, MN, station and the Little Cedar River near 

Ionia, IA, station were calibrated based on streamflow-gaging 

station data from the Cedar River at Janesville, IA, station; 

subbasins originally calibrated on streamflow-gaging station 

data from the Winnebago River at Mason City, IA, station 

were calibrated based on streamflow-gaging station data from 

the Shell Rock River at Shell Rock, IA, station; subbasins 

originally calibrated based on streamflow-gaging station data 

from the Beaver Creek at New Hartford, IA, station and the 

Black Hawk Creek at Hudson, IA, station were calibrated 

based on streamflow-gaging station data from the Cedar River 

at Waterloo, IA, station; and subbasins originally calibrated 

based on streamflow-gaging station data from the Wolf Creek 

near Dysart, IA, station were calibrated based on streamflowgaging station data from the Cedar River at Cedar Rapids, IA, 

station. Locations used for calibration and validation purposes 

for the original and alternative scenarios are listed in table 11.

ENS, R2

, and PBIAS values were determined for hydrology calibration, 2000–04 (table 12), and validation, 2005–10 

(table 13), for all streamflow-gaging stations to see how well 

values at the removed locations, calibrated based on alternative streamflow-gaging stations, compared to results when all 

streamflow-gaging stations were used. Monthly ENS values 

indicate good to very good model performance for all locations for calibration and validation. However, the monthly 

calibration PBIAS for the Winnebago River at Mason City, IA, 

station (-30 percent), and subsequently the Shell Rock River at 

Shell Rock, IA, station (-28 percent), indicates unsatisfactory 

model performance. The monthly calibration and validation 

PBIAS for all other locations indicates satisfactory to very 

good model performance. 

Calibration resulted in annual ENS values ranging from 

0.29 for the Winnebago River at Mason City, IA, station to 

0.92 for the West Fork Cedar River at Finchford, IA, station 

and annual calibration R2 values ranging from 0.65 for the 

Cedar River near Austin, MN, station to 0.99 for the West 

Fork Cedar River at Finchford, IA, station and the Cedar River 

near Conesville, IA, station. Annual calibration PBIAS ranges 

from -31 percent for the Winnebago River at Mason City, IA, 

station to 8 percent for the Black Hawk Creek at Hudson, IA, 

station. 

Monthly calibration ENS values range from 0.70 for the 

Cedar River near Austin, MN, station to 0.91 for the Cedar 

River at Cedar Rapids, IA, station and the Cedar River near 

Conesville, IA, station while monthly calibration R2

 values 

range from 0.72 for the Cedar River near Austin, MN, station to 0.93 for the Cedar River at Cedar Rapids, IA, station. 

Monthly calibration PBIAS ranges from -30 percent for the 

Winnebago River at Mason City, IA, station to 14 percent for 

the Black Hawk Creek at Hudson, IA, station. 

Daily calibration ENS values range from 0.39 for the 

Cedar River near Austin, MN, station to 0.81 for the Cedar 

River near Conesville, IA, station while daily calibration R2

values range from 0.56 for the Wolf Creek near Dysart, IA, 

station to 0.86 for the Cedar River at Cedar Rapids, IA, station. The daily calibration PBIAS ranges from -31 percent for 

the Winnebago River at Mason City, IA, station to 8 percent 

for the Black Hawk Creek at Hudson, IA, station. 

Table 11. List of streamflow-gaging stations used for the original and alternative scenario calibrations, and the streamflow-gaging 

stations used in place of the removed streamflow-gaging stations for calibration in the alternative scenario for the Cedar River Basin 

model, Iowa. 

Original calibration locations Alternative scenario calibration locations New calibration point for alternative 

scenario

Cedar River near Austin, Minnesota Cedar River at Janesville, Iowa.

Winnebago River at Mason City, Iowa Shell Rock River at Shell Rock, Iowa. 

Little Cedar River near Ionia, Iowa Cedar River at Janesville, Iowa.

Shell Rock River at Shell Rock, Iowa Shell Rock River at Shell Rock, Iowa

West Fork Cedar River at Finchford, Iowa West Fork Cedar River at Finchford, Iowa

Cedar River at Janesville, Iowa Cedar River at Janesville, Iowa

Beaver Creek at New Hartford, Iowa Cedar River at Waterloo, Iowa.

Cedar River at Waterloo, Iowa Cedar River at Waterloo, Iowa

Black Hawk Creek at Hudson, Iowa Cedar River at Waterloo, Iowa.

Wolf Creek near Dysart, Iowa Cedar River at Cedar Rapids, Iowa.

Cedar River at Cedar Rapids, Iowa Cedar River at Cedar Rapids, Iowa

Cedar River near Conesville, Iowa Cedar River near Conesville, Iowa
Hydrology and Water Quality Simulation 29

Table 12. Hydrology calibration (January 1, 2000, to December 31, 2004) results for each streamflow-gaging station for the alternative 

scenario for the Cedar River Basin model, Iowa.

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Cedar River near Austin, Minnesota

Daily 0.39 0.57 2% 43 15,000 325 122 4 22,012 319 107

Monthly 0.7 0.72 3% 48 2,328 325 142 14 2,148 315 146

Annual 0.55 0.65 2% 166 457 325 393 194 490 319 223

Winnebago River at Mason City, Iowa

Daily 0.5 0.74 -31% 17 7,550 359 127 11 9,810 472 193

Monthly 0.78 0.88 -30% 28 2,510 359 151 19 2,378 466 220

Annual 0.29 0.93 -31% 237 555 359 249 312 665 472 415

Little Cedar River near Ionia, Iowa

Daily 0.66 0.69 -18% 12 7,530 197 61 5 4,506 231 90

Monthly 0.88 0.89 -17% 18 1,636 196 70 9 1,256 230 123

Annual 0.8 0.96 -17% 84 303 197 202 140 339 231 220

Shell Rock River at Shell Rock, Iowa

Daily 0.54 0.75 -29% 142 23,900 1,175 475 71 27,358 1,514 714

Monthly 0.82 0.9 -28% 174 8,236 1,173 549 103 7,248 1,496 980

Annual 0.37 0.89 -29% 657 1,774 1,174 901 1,051 2,177 1,514 1,265

West Fork Cedar River at Finchford, Iowa

Daily 0.8 0.81 -9% 32 11,300 539 210 24 7,066 589 268

Monthly 0.9 0.91 -10% 64 2,959 537 219 45 3,055 575 312

Annual 0.92 0.99 -9% 381 939 539 407 455 938 589 472

Cedar River at Janesville, Iowa

Daily 0.64 0.75 -7% 183 20,900 1,173 498 32 32,825 1,254 479

Monthly 0.87 0.89 -6% 219 8,056 1,172 542 55 7,153 1,247 611

Annual 0.89 0.93 -7% 577 1,698 1,173 1,202 785 1,862 1,254 1,097

Beaver Creek at New Hartford, Iowa

Daily 0.72 0.72 -12% 9 4,780 191 75 24 4,266 214 111

Monthly 0.8 0.82 -9% 21 920 190 81 32 700 207 135

Annual 0.65 0.81 -13% 120 260 191 179 168 307 214 174

Cedar River at Waterloo, Iowa

Daily 0.69 0.83 -11% 340 57,100 3,444 1,760 198 60,635 3,834 1,830

Monthly 0.89 0.92 -10% 628 19,412 3,437 1,863 302 18,639 3,777 2,245

Annual 0.85 0.97 -11% 2,175 4,837 3,443 2,924 2,710 5,194 3,833 3,369

Black Hawk Creek at Hudson, Iowa1

Daily 0.67 0.68 8% 6 5,450 125 50 3 1,793 113 37

Monthly 0.74 0.79 14% 14 793 124 57 13 521 107 66

Annual 0.87 0.97 8% 83 191 132 122 56 185 122 124
30 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

Annual validation ENS values range from -0.91 for the 

Shell Rock River at Shell Rock, IA, station to 0.95 for the 

West Fork Cedar River at Finchford, IA, station while annual 

validation R2 values range from 0.38 for the Winnebago River 

at Mason City, IA, station to 0.92 for the Black Hawk Creek at 

Hudson, IA, station. Annual validation PBIAS ranges from -23 

percent for the Shell Rock River at Shell Rock, IA, station to 

15 percent for the Black Hawk Creek at Hudson, IA, station. 

Monthly validation ENS values range from 0.68 for the 

Cedar River near Austin, MN, station to 0.90 for the Little 

Cedar River near Ionia, IA, station while monthly validation 

R2

 values range from 0.74 for the Wolf Creek near Dysart, 

IA, station to 0.92 for the Little Cedar River near Ionia, IA, 

station. Monthly validation PBIAS ranges from -23 percent for 

the Shell Rock River at Shell Rock, IA, station to 15 percent 

for the Black Hawk Creek at Hudson, IA, station. 

Daily validation ENS values range from 0.43 for the Cedar 

River near Austin, MN, station to 0.75 for the Cedar River at 

Waterloo, IA, station and the Cedar River at Cedar Rapids, IA, 

station while daily validation R2 values range from 0.60 for 

the Cedar River near Austin, MN, station to 0.83 for the Cedar 

River at Waterloo, IA, station. Daily validation PBIAS ranges 

from -23 percent for the Shell Rock River at Shell Rock, 

IA, station to 14 percent for the Black Hawk at Hudson, IA, 

station. 

The ENS values for all time steps for calibration and validation for the model outlet, the Cedar River near Conesville, 

IA, station ranged from 0.71 to 0.91, while R2

 values ranged 

from 0.78 to 0.99, both just a slight drop from the original 

scenario. Although ENS and R2 values decrease for most locations and time steps relative to the original scenario, there are 

increases in these values for some locations. The Winnebago 

River at Mason City, IA, station is the location for which 

there is the greatest decrease in performance relative to the 

original scenario for the calibration and validation periods; the 

greatest decrease in model performance for this location is at 

the annual time step. In addition, this location, along with the 

Shell Rock River at Shell Rock, IA, station are the only locations to drop from satisfactory or better model performance to 

unsatisfactory model performance as indicated by the monthly 

calibration PBIAS. 

A decrease in values from the original scenario was 

expected and can be attributed to a number of factors, such 

as projecting calibration parameters from one subbasin to 

another subbasin that has vastly different physical characteristics or land cover and management practices, or both. For 

example, the Winnebago River at Mason City, IA, station 

drains part of the Des Moines lobe landform region, while the 

rest of the subbasin is physically defined as Iowan Surface. 

This could explain the substantial decline in model performance for this location relative to the original scenario. As 

an additional example, the subbasins contributing directly to 

the Cedar River at Waterloo, IA, station have distinct physical differences from those subbasins contributing to the Black 

Hawk Creek at Hudson, IA, station and Beaver Creek at New 

Hartford, IA, station which were calibrated based on the Cedar 

Table 12. Hydrology calibration (January 1, 2000, to December 31, 2004) results for each streamflow-gaging station for the alternative 

scenario for the Cedar River Basin model, Iowa.—Continued

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Wolf Creek near Dysart, Iowa2

Daily 0.53 0.56 1% 7 8,360 123 40 0 1,794 121 52

Monthly 0.75 0.83 6% 13 975 126 44 9 514 118 78

Annual 0.82 0.74 -4% 54 214 125 117 52 185 130 142

Cedar River at Cedar Rapids, Iowa

Daily 0.78 0.86 -12% 326 61,800 4,200 2,240 263 57,987 4,690 2,450

Monthly 0.91 0.93 -10% 722 21,148 4,193 2,372 474 20,250 4,612 2,722

Annual 0.85 0.98 -12% 2,716 6,172 4,200 3,639 3,345 6,306 4,689 4,081

Cedar River near Conesville, Iowa

Daily 0.81 0.85 -10% 660 69,200 5,052 2,760 371 56,998 5,546 3,292

Monthly 0.91 0.92 -8% 1,029 22,207 5,045 2,839 643 21,476 5,455 3,420

Annual 0.89 0.99 -10% 3,568 7,092 5,052 4,249 3,937 7,440 5,546 4,646

1

Measured data was unavailable for 2000 and a part of 2001; calibration statistics are based on a total of 1,212 measured daily values. 

2

Measured data was unavailable for 2000 and a part of 2001; calibration statistics are based on a total of 1,326 measured daily values. 
Hydrology and Water Quality Simulation 31

Table 13. Hydrology validation (January 1, 2005, to December 31, 2010) results for each streamflow-gaging station for the alternative 

scenario for the Cedar River Basin model, Iowa.

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Cedar River near Austin, Minnesota1

Daily 0.43 0.60 -5% 49 11,500 350 175 17 10,418 369 141

Monthly 0.68 0.79 -6% 58 1,606 349 227 32 2,313 368 244

Annual 0.70 0.75 -5% 222 462 349 346 278 500 368 364

Winnebago River at Mason City, Iowa

Daily 0.61 0.75 -17% 27 10,400 464 241 28 11,078 542 276

Monthly 0.81 0.85 -17% 63 2,795 464 315 62 2,621 541 357

Annual -0.57 0.38 -17% 314 582 464 467 391 680 542 550

Little Cedar River near Ionia, Iowa

Daily 0.62 0.64 -15% 17 21,400 265 116 18 10,058 305 126

Monthly 0.90 0.92 -15% 26 2,551 265 174 32 2,091 305 197

Annual 0.54 0.83 -15% 183 396 265 251 206 422 305 287

Shell Rock River at Shell Rock, Iowa

Daily 0.53 0.73 -23% 247 46,400 1,539 831 136 36,904 1,888 951

Monthly 0.73 0.85 -23% 289 9,999 1,538 1,111 203 10,415 1,886 1,301

Annual -0.91 0.49 -23% 1,095 2,024 1,539 1,521 1,415 2,438 1,888 1,817

West Fork Cedar River at Finchford, Iowa

Daily 0.58 0.77 -8% 43 23,300 955 492 39 20,811 1,028 463

Monthly 0.79 0.84 -8% 64 5,315 954 570 56 5,997 1,026 730

Annual 0.95 0.75 -8% 528 1,279 955 1,057 687 1,325 1,028 1,060

Cedar River at Janesville, Iowa

Daily 0.67 0.75 -6% 281 51,400 1,579 840 88 31,677 1,666 738

Monthly 0.84 0.87 -5% 322 10,778 1,581 1,129 122 10,234 1,667 1,126

Annual 0.72 0.78 -6% 1,157 2,176 1,579 1,548 1,307 2,191 1,666 1,512

Beaver Creek at New Hartford, Iowa

Daily 0.53 0.65 4% 26 15,700 443 213 32 15,655 426 187

Monthly 0.83 0.83 4% 38 2,917 443 297 42 2,199 425 287

Annual 0.83 0.84 4% 183 635 443 508 223 610 425 441

Cedar River at Waterloo, Iowa

Daily 0.75 0.83 -4% 710 104,000 5,366 3,040 398 97,998 5,589 2,744

Monthly 0.86 0.88 -4% 38 2,917 443 297 603 32,065 5,584 3,753

Annual 0.74 0.77 -4% 3,432 7,351 5,365 5,492 3,904 7,150 5,588 5,413

Black Hawk Creek at Hudson, Iowa

Daily 0.57 0.68 14% 9 10,600 381 192 12 13,639 328 130

Monthly 0.79 0.82 15% 11 2,102 384 244 17 2,385 328 193

Annual 0.82 0.92 15% 138 597 385 456 114 524 328 375
32 Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin

River at Waterloo , IA, station parameters; the Cedar River at 

Waterloo, IA, station has a large urban contribution.

Summary

The U.S. Geological Survey, in cooperation with the Iowa 

Department of Natural Resources, used the Soil and Water 

Assessment Tool to simulate streamflow and nitrate loads 

within the Cedar River Basin, Iowa. The goal was to assess 

the ability of the Soil and Water Assessment Tool to estimate 

streamflow and nitrate loads in gaged and ungaged basins in 

Iowa. The Cedar River basin model uses measured streamflow data from 12 U.S. Geological Survey streamflow-gaging 

stations for hydrology calibration. The nitrate calibration was 

based on a small subset of the locations used in the hydrology 

calibration and uses nitrate concentration and corresponding 

streamflow from three Iowa Storage and Retrieval/Water 

Quality Exchange STORET/WQX stations. Streamflow 

and nitrate loads were calibrated for the period of January 1, 

2000, to December 31, 2004, and validated for the period of 

January 1, 2005, to December 31, 2010. 

Daily, monthly, and annual ENS, R2

, and PBIAS values 

were determined for hydrology calibration and validation 

for all 12 streamflow-gaging station locations and illustrate 

the capability of SWAT for predicting hydrology; calibration 

ENS and R2

 values are greater than 0.5 for all locations and 

time steps with the exception of the Cedar River near Austin, 

MN, streamflow-gaging station while PBIAS results indicate 

satisfactory to very good performance for all locations. 

Monthly validation ENS values indicate good to very good 

performance, while PBIAS results range from satisfactory to 

very good. 

The nitrate load calibration period resulted in annual and 

monthly ENS and R2 values greater than 0.6 for the Shell Rock 

River at Shell Rock, IA, streamflow-gaging station and the 

Cedar River near Conesville, IA, streamflow-gaging station 

with monthly values indicating good to very good performance, respectively. Although the annual and monthly calibration R2

 for the Cedar River at Janesville, IA, streamflowgaging station were greater than 0.6, the monthly calibration 

ENS indicated unsatisfactory performance. PBIAS results for 

the calibration period range from 4 percent for the Cedar River 

near Conesville, IA, streamflow-gaging station to 7 percent for 

the Cedar River at Janesville, IA, streamflow-gaging station. 

Monthly and annual validation ENS values indicate that the 

measured mean is actually a better predictor than the model 

and that the model cannot accurately simulate nitrate loads 

for the 2005–10 time period. Nitrate loads were substantially 

underestimated for the validation period. A major limitation 

for successful nitrate load calibration is applying uniform 

management operations year to year, basinwide. While management operations such as planting and fertilizer application 

will vary from field to field and from year to year, lack of this 

information as well as the time requirement for implementing 

management operations at a finer resolution requires generic 

application. Depending on the year this could cause substantial differences between actual and simulated management 

operations. 

Table 13. Hydrology validation (January 1, 2005, to December 31, 2010) results for each streamflow-gaging station for the alternative 

scenario for the Cedar River Basin model, Iowa.—Continued

[ENS, Nash-Sutcliffe coefficient of model efficiency; R2, coefficient of determination ; PBIAS, percent bias; ft3/s, cubic feet per second; %, percent]

ENS R2 PBIAS

Measured Simulated

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Min 

streamflow (ft3

/s)

Max 

streamflow (ft3

/s)

Mean 

streamflow (ft3

/s)

Median 

streamflow (ft3

/s)

Wolf Creek near Dysart, Iowa

Daily 0.58 0.66 11% 13 9,400 362 182 11 10,877 323 132

Monthly 0.71 0.74 11% 21 2,001 362 239 18 2,224 322 199

Annual 0.83 0.89 11% 100 625 362 399 102 527 322 375

Cedar River at Cedar Rapids, Iowa

Daily 0.75 0.80 -5% 916 138,000 6,771 3,940 562 119,364 7,188 3,849

Monthly 0.84 0.86 -5% 1,506 46,453 6,765 5,190 915 41,389 7,178 5,238

Annual 0.79 0.82 -5% 3,801 10,139 6,770 7,016 4,723 9,757 7,187 7,293

Cedar River near Conesville, Iowa

Daily 0.71 0.78 0% 983 119,000 8,490 5,170 770 133,136 8,456 4,704

Monthly 0.84 0.85 0% 1,658 47,687 8,475 6,087 1,661 47,291 8,444 6,387

Annual 0.85 0.88 0% 4,327 12,935 8,488 9,145 5,041 11,793 8,455 9,134

1

Measured data is missing for December 10, 2009, to December 31, 2009; validation statistics are based on 2,147 measured daily values.
References Cited 33

An alternative hydrology calibration scenario was run 

to represent the situation with regard to streamflow-gaging 

station density, and thus calibration points, for application to 

other Iowa basins. This scenario involved removing a subset 

of the streamflow-gaging stations that had been incorporated 

in the first calibration retaining only those streamflow-gaging 

stations located on the main stem of the Cedar River. As 

expected, ENS and R2 values were highest for the original 

scenario in which all locations were used. However, statistical values remained high in the alternative scenario. For many 

of the locations and time steps, modifications of the calibration parameters had minimal effects on the results. Monthly 

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estimate streamflow in less densely gaged basins throughout 

the state, especially at the monthly time step, but that caution 

should be used when calibrating a location based on one with 

known physical dissimilarities. 

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Publishing support provided by:

Rolla Publishing Service Center

For more information concerning this publication, contact:

Director, USGS Iowa Water Science Center

P.O. Box 1230

Iowa City, IA 52244

(319) 337–4191

Or visit the Iowa Water Science Center Web site at:

http://ia.water.usgs.gov

Hutchinson and other—Use of the Soil and Water Assessment Tool (SWAT) for Simulating Hydrology and Water Quality in the Cedar River Basin—Scientific Investigations Report 2013–5002