Scientific Investigations Report 2009–5030

Effect of Agricultural Practices on Hydrology and 

Water Chemistry in a Small Irrigated Catchment, 

Yakima River Basin, Washington

U.S. Department of the Interior

U.S. Geological Survey

National Water-Quality Assessment Program
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Effect of Agricultural Practices on Hydrology and 

Water Chemistry in a Small Irrigated Catchment, 

Yakima River Basin, Washington

By Kathleen A. McCarthy and Henry M. Johnson

Scientific Investigations Report 2009–5030

U.S. Department of the Interior

U.S. Geological Survey

National Water-Quality Assessment Program
U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2009

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reproduce any copyrighted materials contained within this report.

Suggested citation:

McCarthy, K.A., and Johnson, H.M., 2009, Effect of agricultural practices on hydrology and water chemistry in a 

small irrigated catchment, Yakima River basin, Washington: U.S. Geological Survey Scientific Investigations 

Report 2009-5030, 22 p.
iii

Foreword

The U.S. Geological Survey (USGS) is committed to providing the Nation with credible scientific information 

that helps to enhance and protect the overall quality of life and that facilitates effective management of water, 

biological, energy, and mineral resources (http://www.usgs.gov/). Information on the Nation’s water resources 

is critical to ensuring long-term availability of water that is safe for drinking and recreation and is suitable 

for industry, irrigation, and fish and wildlife. Population growth and increasing demands for water make the 

availability of that water, now measured in terms of quantity and quality, even more essential to the long-term 

sustainability of our communities and ecosystems.

The USGS implemented the National Water-Quality Assessment (NAWQA) Program in 1991 to support national, 

regional, State, and local information needs and decisions related to water-quality management and policy 

(http://water.usgs.gov/nawqa). The NAWQA Program is designed to answer: What is the condition of our 

Nation’s streams and ground water? How are conditions changing over time? How do natural features and 

human activities affect the quality of streams and ground water, and where are those effects most pronounced? 

By combining information on water chemistry, physical characteristics, stream habitat, and aquatic life, the 

NAWQA Program aims to provide science-based insights for current and emerging water issues and priorities. 

From 1991–2001, the NAWQA Program completed interdisciplinary assessments and established a baseline 

understanding of water-quality conditions in 51 of the Nation’s river basins and aquifers, referred to as Study 

Units (http://water.usgs.gov/nawqa/studyu.html). 

Multiple national and regional assessments are ongoing in the second decade (2001–2012) of the NAWQA 

Program as 42 of the 51 Study Units are reassessed. These assessments extend the findings in the Study Units 

by determining status and trends at sites that have been consistently monitored for more than a decade, and 

filling critical gaps in characterizing the quality of surface water and ground water. For example, increased 

emphasis has been placed on assessing the quality of source water and finished water associated with many 

of the Nation’s largest community water systems. During the second decade, NAWQA is addressing five 

national priority topics that build an understanding of how natural features and human activities affect water 

quality, and establish links between sources of contaminants, the transport of those contaminants through the 

hydrologic system, and the potential effects of contaminants on humans and aquatic ecosystems. Included are 

topics on the fate of agricultural chemicals, effects of urbanization on stream ecosystems, bioaccumulation 

of mercury in stream ecosystems, effects of nutrient enrichment on aquatic ecosystems, and transport of 

contaminants to public-supply wells. These topical studies are conducted in those Study Units most affected by 

these issues; they comprise a set of multi-Study-Unit designs for systematic national assessment. In addition, 

national syntheses of information on pesticides, volatile organic compounds (VOCs), nutrients, selected trace 

elements, and aquatic ecology are continuing. 

The USGS aims to disseminate credible, timely, and relevant science information to address practical and 

effective water-resource management and strategies that protect and restore water quality. We hope this 

NAWQA publication will provide you with insights and information to meet your needs, and will foster 

increased citizen awareness and involvement in the protection and restoration of our Nation’s waters. 

The USGS recognizes that a national assessment by a single program cannot address all water-resource 

issues of interest. External coordination at all levels is critical for cost-effective management, regulation, 

and conservation of our Nation’s water resources. The NAWQA Program, therefore, depends on advice 

and information from other agencies—Federal, State, regional, interstate, Tribal, and local—as well as 

nongovernmental organizations, industry, academia, and other stakeholder groups. Your assistance and 

suggestions are greatly appreciated.

Matthew C. Larsen

Associate Director for Water
iv

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v

Contents

Foreword ........................................................................................................................................................iii

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

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

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

Study Methods ...............................................................................................................................................2

Collection and Analysis of Hydrologic Data.....................................................................................2

Collection and Analysis of Water-Chemistry Data..........................................................................4

Effects of Agricultural Practices.................................................................................................................5

Hydrology ...............................................................................................................................................5

Water Chemistry .................................................................................................................................11

Inverse End-Member Mixing Analysis............................................................................................18

Summary and Conclusions.........................................................................................................................21

Acknowledgments.......................................................................................................................................21

References Cited .........................................................................................................................................21

Figures

Figure 1. Map showing location of the DR2 catchment and data-collection sites,

Yakima River basin, Washington ......................................................... 3

Figure 2. Graph showing data-collection dates in the DR2 catchment, Yakima River

basin, Washington........................................................................... 4

Figure 3. Graph showing estimated 2003 water balance for the DR2 catchment, Yakima

River basin, Washington .................................................................. 5

Figure 4. Hydrograph showing discharge for the DR2 Catchment surface-water

outflow (site W13), Yakima River basin, Washington.................................... 6

Figure 5. Diagram showing conceptualization of the hydrology of the DR2 catchment,

Yakima River basin, Washington ......................................................... 7

Figure 6. Graphs showing wWater levels in well pairs in the DR2 catchment, Yakima

River basin, Washington .................................................................. 8

Figure 7. Graphs showing water levels and water temperatures in ground water in the

DR2 catchment, Yakima River basin, Washington. .................................... 9

Figure 8. Graph showing ground-water head gradient (black line) and temperature

(grey line) at site W23, DR2 catchment, Yakima River basin, Washington............ 9

Figure 9. Graph showing estimated ground-water recharge dates in the DR2

catchment, Yakima River basin, Washington............................................. 10

Figure 10. Graph showing abundance of deuterium and oxygen–18 in water samples

from the DR2 catchment, Yakima River basin, Washington ........................... 11

Figure 11. Graph showing abundances of oxygen-18 and nitrogen-15 in nitrate in water

samples from the DR2 catchment, Yakima River basin, Washington.................. 12

Figure 12. Boxplot showing distribution of specific conductance of water samples from

the DR2 catchment, Yakima River basin, Washington ................................. 12

Figure 13. Boxplots showing distribution of concentrations of major solutes in water

samples from the DR2 catchment, Yakima River basin, Washington.................. 13
vi

Conversion Factors and Datums

Conversion Factors

Multiply By To obtain

centimeter (cm) 0.3937 inch (in.)

kilometer (km) 0.6214 mile (mi)

liter (L) 33.82 ounce, fluid (fl. oz)

liter (L) 0.2642 gallon (gal)

meter (m) 3.281 foot (ft) 

cubic meters per second (m3/s) 35.31 cubic feet per second (ft3/s) 

millimeter (mm) 0.03937 inch (in.)

square kilometer (km2) 247.1 acre

square kilometer (km2) 0.3861 square mile (mi2)

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

°F=(1.8×°C)+32.

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 25°C).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) or 

micrograms per liter (μg/L).

Datums

Vertical coordinate information is referenced the North American Vertical Datum of 1988 (NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27).

Figures—Continued

Figure 15. Graph showing vertical temperature profile measured in the streambed in the DR2 

catchment, Yakima River basin, Washington, September 2004 ........................ 16

Figure 14. Boxplots showing distribution of concentrations of nitrate and soluble

reactive phosphorus in water samples from the DR2 catchment, Yakima

River basin, Washington .................................................................. 16

Figure 16. Graphs showing concentrations of selected solutes (square symbols) and

stream discharge (solid line) at the DR2 catchment outflow (site W13),

Yakima River basin, Washington ......................................................... 17

Figure 17. Boxplots showing distribution of concentrations of selected solutes

measured in the DR2 catchment outflow components, and concentrations

calculated for hypothetical seasonal agricultural flow (SAF), Yakima River

basin, Washington........................................................................... 20

Tables

Table 1. Excess nitrogen gas (N2) measured in the DR2 catchment, Yakima River

basin, Washington........................................................................... 15

Table 2. Composition of surface flow-system components during the irrigation

season in the DR2 catchment, Yakima River basin, Washington ..................... 19
Effect of Agricultural Practices on Hydrology and 

Water Chemistry in a Small Irrigated Catchment, 

Yakima River Basin, Washington

Introduction

Agriculture is widely recognized as a major source of 

nutrients and other potential contaminants to water bodies 

throughout the world. In an assessment of the effects of human 

activity on water quality, the U.S. Environmental Protection 

Agency (2002, 2005) listed agricultural practices and 

hydrological modifications as the two most important causes 

of water-quality impairment to streams assessed during the 

2000 National Water-Quality Inventory. Because irrigation can 

extensively modify the hydrology of small catchments, these 

findings indicate that irrigated agriculture may be of particular 

importance as a source of water-quality impairment.

In the Western United States, between one-quarter and 

one-third of harvested cropland is irrigated (Schaible, 2004). 

Due to the nature of the crops and relatively high yields, 

however, this irrigated cropland accounts for approximately 

three-quarters of the value of crops sold in the West (Gollehon 

and Quinby, 2000). It is estimated that the global demand for 

food will more than double over the coming decades (Green 

and others, 2005), and it is likely that much of the increased 

demand will be met by irrigated agriculture.

In the Western United States, irrigation is typically 

applied to naturally arid or semiarid landscapes, where few 

natural surface drainage routes exist. To keep such areas 

agriculturally productive, artificial surface and shallow 

subsurface drainage networks often are constructed to 

facilitate runoff. In many of these networks, virtually all water 

carried by the drains is agricultural runoff, and little or no 

dilution from naturally occurring ground-water base flow or 

storm-generated surface runoff occurs. As a result, in addition 

to the diffuse nonpoint-source contamination typically 

associated with agriculture, drainage networks in irrigated 

areas can act as point sources of contaminants to receiving 

streams and lakes.

By Kathleen A. McCarthy and Henry M. Johnson

Abstract

The role of irrigation and artificial drainage in the 

hydrologic cycle and the transport of solutes in a small 

agricultural catchment in central Washington’s Yakima Valley 

were explored using hydrologic, chemical, isotopic, agedating, and mineralogical data from several environmental 

compartments, including stream water, ground water, overland 

flow, and streambed pore water. A conceptual understanding of 

catchment hydrology and solute transport was developed and 

an inverse end-member mixing analysis was used to further 

explore the effects of agriculture in this small catchment. The 

median concentrations of major solutes and nitrates were 

similar for the single field site and for the catchment outflow 

site, indicating that the net effects of transport processes 

for these constituents were similar at both scales. However, 

concentrations of nutrients were different at the two sites, 

suggesting that field-scale variations in agricultural practices 

as well as nearstream and instream biochemical processes are 

important components of agricultural chemical transformation 

and transport in this catchment. This work indicates that 

irrigation coupled with artificial drainage networks may 

exacerbate the ecological effects of agricultural runoff by 

increasing direct connectivity between fields and streams and 

minimizing potentially mitigating effects (denitrification and 

dilution, for example) of longer subsurface pathways.
2 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

In the work presented here, the hydrologic cycle and 

the transport of solutes in a small, irrigated catchment in 

the Yakima Valley of central Washington are described on 

the basis of the results of analyses of various hydrologic, 

chemical, isotopic, age dating, and mineralogical data from 

several environmental compartments, including stream water, 

ground water, overland flow, and streambed pore water. A 

conceptual model of catchment hydrology and solute transport 

is developed and an inverse end-member mixing analysis is 

used to further explore the effects of agriculture in this small 

irrigated catchment.

These data were collected as part of a larger effort by 

the U.S. Geological Survey (USGS) National Water-Quality 

Assessment (NAWQA) program. To gain insights into how 

environmental processes and agricultural practices interact 

to determine the transport and fate of agricultural chemicals 

in the environment, the USGS NAWQA program conducted 

in-depth investigations at five agricultural study areas across 

the country during 2003–04. The design of the overall study 

is described in detail by Capel and others (2008). Companion 

studies report on the transport and processing of agricultural 

chemicals in surface water (Domagalski and others, 2008; 

Duff and others, 2008); transport in the subsurface (Green 

and others, 2008; Steele and others, 2008), and ground-water/

surface-water interactions (Duff and others, 2008; Essaid and 

others, 2008; Puckett and others, 2008).

Description of Study Area

The DR2 catchment is a small (5.5 km2) subbasin in 

the Yakima Valley of central Washington (fig. 1). A detailed 

description of the catchment is available in Payne and others 

(2007). Three characteristics of the catchment particularly 

relevant to the transport and fate of agricultural chemicals are: 

(1) irrigation practices, (2) crop heterogeneity, and (3) subsurface 

drainage. These characteristics are discussed here briefly.

Land use in the DR2 catchment is nearly 90 percent 

agriculture, and, with less than 18 cm of annual precipitation, 

95 percent of the agriculture is irrigated. The demand for 

irrigation water is met by withdrawals from the Yakima River 

that are delivered to the catchment through the Sunnyside 

Canal (fig. 1) and dispersed throughout the catchment by 

secondary delivery canals. At the individual field scale, water 

is applied to crops by various methods, including rill, drip, 

and sprinkler systems. Although the use of rill irrigation 

is slowly diminishing in the catchment as growers convert 

to more efficient sprinkler and drip systems, it remains the 

predominant method due to economic, planting, harvesting, 

and other crop management considerations that make more 

efficient systems less practical.

A wide variety of crops are grown in the DR2 catchment 

(Payne and others, 2007). During the study period, crops and 

other agricultural activities included corn, grapes (for both 

wine and juice), asparagus, alfalfa, forage grass, pasture, 

and dairy/feedlot operations. Not only do crops—and 

therefore irrigation practices and chemical applications—vary 

considerably across this small catchment, they also vary from 

year to year in many fields.

Shallow subsurface flow in the area has been modified 

by an extensive system of buried drains. These drains exert a 

strong influence on the shallow ground-water system and its 

connection to surface water. However, most of the drainage 

system has been in place for many decades, and apart from the 

large, regional drains, the location and extent of the drains are 

not well known. 

Study Methods

Hydrologic and water-quality data were collected from 

38 sites in the study area: the irrigation delivery canal (W15), 

18 wells (W20p–W32q), 17 streambed sites in 2 transects 

located near the mouth of DR2 (W51a-W64c), a field drain 

(W42), and the surface-water outflow of DR2 (W13) (fig. 1). 

Data collected included ground-water levels, stream stage, 

stream discharge, water-quality parameters, estimated groundwater recharge dates, stable isotope abundances in water and 

nitrate, and soil mineralogy.

Collection and Analysis of Hydrologic Data

Wells, piezometers, and drive points used for collection of 

ground-water and streambed data were installed as part of this 

study, following procedures described in Lapham and others 

(1997). Wells were constructed of 5-cm-diameter PVC with 

1.5-m slotted PVC screens and were installed using either a 

hollow-stem auger or a mud rotary drill. The annulus around the 

screen was filled with silica sand, the remaining annulus was 

grouted with bentonite, and a cement cap was placed at land 

surface. Shallow wells were generally screened approximately 

1 m or less below the water table; deeper wells were screened 

7–12 m below the water table except at site W21, where wells 

also were screened at 16 and 26 m below the water table.

Piezometers and drive points at the streambed transects 

were installed in 10-cm-diameter hand-augered holes. 

Piezometers for measuring water levels had screened open 

intervals of 15 cm, and drive points for water-sample collection 

had screened open intervals of 0.95 cm. The annular space was 

filled with sand to a height of approximately 6–15 cm above the 

top of the screen and then with bentonite pellets to the level of 

the streambed. During well installation at most sites, samples 

of aquifer material were collected with a split-spoon sampler 

from the depth of the screened interval and submitted for 

mineralogical analysis by X-ray diffraction. After installation, 

wells were developed by pumping and surging and were allowed 

to equilibrate for at least 45 days before the first water samples 

were collected. Additional installation details are described by 

Capel and others (2008) and Puckett and others (2008). 
Description of Study Area 3

Figure 1. Location of the DR2 catchment and data-collection sites, Yakima River basin, Washington.

OR090263SpragueMcCarthyFig01

224

226

228

224

226

228

HORIZONTAL COORDINATE, IN METERS

ELEVATION, IN METERSELEVATION, IN METERS

UPSTREAM TRANSECT DOWNSTREAM TRANSECT

7 6 5 4 3 2 1 0

HORIZONTAL COORDINATE, IN METERS

7 6 5 4 3 2 1 0

W61b

W62c

W62b

W63c

W63a W64a

W64c W61c

W55b

W55c

W53a

W52a

W52b

W51a

W51c

W54a

W53b

West West

Granger Drain

Sunnyside Canal

12

82

Van Belle Road

Wellner Road

Independence Road

Dekker Road

Arms Road

Lowry Road

Price Road

Norht Outlook Road

A

A’

W42

W25p,q

W24p,q

W31p,q

W13

W22p

W20p,q

W23p,q

W32p,q

W30p

W21p,q,r,s

W15

120°08'30" 120°08'00" 120°07'30" 120°07'00" 120°06'30" 120°06'00" 120°05'30"

46°

22'

00"

46°

21'

30"

46°

21'

00"

46°

20'

30"

46°

20'

00"

DR2 Drain

WASHINGTON

Yakima

Basin

Map area

Yakima River

Study area transect

DR2 catchment 

 boundary

Stream or drain

Secondary delivery

 canal

Canal

Crop boundary, 1991

Well

Surface water site

Streambed transect

Site number

EXPLANATION

A A’

W13

Base map modified from USGS NHD, USGS 1:24,000 topo maps, USGS 30-m 

DEM, canals and laterals: Sunnyside Valley Irrigation District, roads: Yakima 

County. Projection: UTM, Zone 10N, datum: North American Datum 1927.

0 2 4 6 8 1,000 FEET

0 1 2 300 METERS
4 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

Water-level data were collected manually from 16 wells, 

and water-level and temperature data were collected by 

electronic recorder from 6 shallow wells, the W23 well pair, 

and 1 streambed site. Recorder data were collected using 

Solinst Leveloggers (Model 3001 F15; range: 4 m; resolution: 

0.1 cm; accuracy: 4 mm; Solinst Canada Ltd, Georgetown, 

Ontario, Canada) and Solinst Barologgers (Model M5), for 

atmospheric-pressure-change compensation. The temperature 

of water in the stream and at multiple depths below the 

streambed was recorded by suspending StowAway TidbiT 

Temperature Loggers (Onset Computer Corp. Pocasset, 

Massachusetts; range: -4 to 30°C; accuracy: ±0.2°C at 20°C) 

within the piezometer clusters. 

Discharge from the field drain was measured 

volumetrically, using a calibrated 19 L bucket and stopwatch. 

Stream discharge was measured near the catchment outlet 

using an AquaRod water-level sensor (Sequoia Scientific, 

Inc., Bellevue, Washington). The AquaRod was mounted in an 

existing, calibrated flume that is maintained by the Sunnyside 

Valley Irrigation District (Sunnyside, Washington). Irrigation 

and canal-leakage data were obtained from the Sunnyside 

Valley Irrigation District. 

Precipitation data and daily crop-specific evapotranspiration data were obtained from the Harrah, Washington, 

station of the Pacific Northwest Cooperative Agricultural 

Weather Network (U.S. Department of the Interior, Bureau 

of Reclamation, Pacific Northwest Region; http://www.usbr.

gov/pn/agrimet/, accessed January 6, 2009), located approximately 35 km from the study catchment. These evapotranspiration data were coupled with field-scale crop data obtained 

from land-use surveys (Payne and others, 2007) to estimate 

total catchment evapotranspiration. (Precipitation data from 

an onsite weather station were available, but the period of 

record was inadequate for use in the work reported here. The 

onsite data that were available agreed well with data from 

Harrah station, with differences in total precipitation less than 

10 percent for the common periods of record.)

The quantities of ground water flowing into and out of 

the catchment were estimated from numerical simulations 

(Leon J. Kauffman, U.S. Geological Survey, written commun., 

2006) using the MODFLOW code (Harbaugh and others, 

2000). Ground-water flow paths were simulated (Leon J. 

Kauffman, U.S. Geological Survey, written commun., 2006) 

using the particle-tracking code MODPATH (Pollock, 1994). 

Collection and Analysis of Water-Chemistry Data

During 2004, water samples were collected 6 times from 

the Sunnyside Canal (W15), 4 times from wells (W20p–

W32q) and streambed sites (W51a–W64c), 17 times from the 

field drain (W42), and 27 times from DR2 at the catchment 

outflow (W13) (fig. 2). Measurements of temperature, pH, 

specific conductance, alkalinity, and dissolved oxygen were 

obtained onsite. Water samples were subsequently analyzed 

for nitrogen (N) and phosphorus (P) species, and for major 

solutes (calcium, magnesium, sodium, potassium, chloride, 

and silica). Selected samples also were analyzed for dissolved 

organic carbon (DOC), stable isotopes of water (2H and 18O), 

and stable isotopes of nitrate (15N and 18O). Selected groundwater and streambed samples were analyzed for age-dating 

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG OCT DEC JAN

2003 2004 2005

SEPT NOV

CANAL (W15)

FIELD DRAIN

(W42)

GROUND WATER

(W20p–W32q)

STREAMBED

TRANSECTS

(W51a–W64c)

BASIN OUTLET

(W13)

Sunnyside Canal empty

Sunnyside Canal flowing

2 3 2 2

2

Numbers above symbols

indicate multiple samples

Figure 2. Data-collection dates in the DR2 catchment, Yakima River basin, Washington.
Effects of Agricultural Practices 5

constituents, including CFCl3 (CFC-11), CF2Cl2 (CFC-12), 

and C2F3Cl3 (CFC-113), sulfur hexafluoride (SF6), and tritium 

(3H), and for concentrations of dissolved N gas (N2) and 

argon in order to estimate the amount of N present as a result 

of denitrification (Heaton and Vogel, 1981; Vogel and others, 

1981; Böhlke and others, 2002; Green and others, 2008). 

Further details of the instrumentation and the methods 

used for data collection, analysis, and quality control are 

described by Capel and others (2008, supplemental material). 

Additional information on sample-collection, analyses, and 

interpretation of dissolved-gas, stable-isotope, and groundwater-age data are available in Green and others (2008). 

Effects of Agricultural Practices

Hydrology

Knowledge of how water moves through a catchment 

is fundamental to understanding the effects of agricultural 

practices. One of the primary objectives of this work, 

therefore, was to develop a conceptual model of the sources, 

distribution, and movement of water within the DR2 

catchment. A simple water balance (fig. 3), estimated from 

2003 data, provides insight into the overall hydrology of the 

catchment and the processes that influence agricultural effects 

on the environment in this study area. 

Irrigation water, imported from the Yakima River, is 

the principal source of water to the catchment, accounting 

for nearly 60 percent of the total inflow. This irrigation 

water is delivered through the Sunnyside Canal (fig. 1) 

and is transported throughout the catchment by a series 

of secondary canals, from which it is applied to crops and 

pasture. Rill irrigation—the predominant application method 

used in the catchment—typically results in 15 to 25 percent 

of the applied water running out the end of the furrows (U.S. 

Environmental Protection Agency, 2003; Eisenhauer and 

others, 2006; Schwankl and others, 2007). This tailwater 

is routed into surface or subsurface drains that eventually 

discharge to regional surface-water drains, such as DR2. 

Sprinkler irrigation—the other major water application method 

in DR2—produces no tailwater in most circumstances. Most 

canal water diverted into the irrigation water delivery system 

is applied to the land surface; however, a small fraction of the 

diverted water goes unused as part of the normal operation 

of the gravity-driven irrigation-water delivery network. This 

end-of-system “operational spill” also is routed into the 

regional drainage network. Additional unused water may enter 

the drainage system due to a lag time between requests for 

changes in the delivery amount and the implementation of the 

request, the onset of unexpected cool or wet weather, system 

malfunctions (such as pipe breaks), and various on-farm 

exigencies. 

Other primary sources of water to the catchment 

are ground water that flows into the area from north of 

the Sunnyside Canal, precipitation, and leakage from 

the Sunnyside Canal. Together, these four major sources 

contribute approximately 180 cm of water per year to the 

catchment. Evapotranspiration and stream discharge account 

for nearly 90 percent of the total catchment outflow. The third 

important component of outflow is ground water.

Irrigation is a key component of the hydrology of the 

DR2 catchment (fig. 3). In fact, there is no evidence that a 

surface-water system existed in the catchment before irrigated 

agriculture began in the area more than a century ago (Payne 

and others, 2007). In addition to creating an extensive surfacewater drainage network during the growing season, long-term 

irrigation has caused ground-water levels to rise, and the 

higher water table provides base flow that sustains the surfacewater flow year-round in the southern part of the catchment.

A hydrograph of the discharge of DR2 near the catchment 

outflow (site W13) shows the influence of the annual 

irrigation cycle (fig. 4). Ground-water levels measured in 

wells throughout the catchment were consistently higher than 

the stage of the water in DR2, indicating that ground water 

flowed toward DR2 at all times. During the nonirrigation 

season (mid-October through mid-March), base flow in the 

stream is sustained by ground water, most of which originated 

as infiltrating irrigation within and upgradient of the DR2 

basin. During the irrigation season (mid-March through midOctober), discharge at site W13 increased two- to threefold. 

The shape of the annual discharge hydrograph is defined by 

the controlled application of irrigation water, and because of 

the absence of major precipitation events, short-term variation 

in stream flow is small and occurs predominantly during the 

irrigation season, driven by crop demands and agricultural 

practices.

Figure 3. Estimated 2003 water balance for the DR2 

catchment, Yakima River basin, Washington.

0

25

50

75

100

IRRIGATION DELIVERIES

GROUND-WATER FLOW

PRECIPITATION

CANAL LEAKAGE

EVAPOTRANSPIRATION

STREAM DISCHARGE

GROUND WATER 

CENTIMETERS PER YEAR

BASIN INFLOWS BASIN OUTFLOWS
6 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

A conceptual model of subsurface flow in the DR2 

catchment was developed on the basis of several lines of 

evidence, including ground-water levels, ground-water age 

estimates, the isotopic composition of water from selected 

sites, visual observations of flow in the surface drainage 

network, and results of numerical ground-water modeling and 

flow-path simulations (Leon J. Kauffman, U.S. Geological 

Survey, written commun., 2006). In this conceptualization, 

regional ground-water generally flows from north to south, 

but the local shallow system is more complex, consisting of 

small-scale subsystems driven by individual irrigation events 

and constrained by local topography and the extensive system 

of artificial drains (both surface and buried) that intercept 

shallow ground water and route it toward the surface-water 

drainage network (fig. 5). While the drain system promotes 

lateral flow to the stream, upward flux of deeper ground water 

through the streambed is limited, especially in the southern 

part of the catchment, by low-permeability streambed material. 

At the streambed transects, permeabilities ranging from 10-5

to 10-6 m/s were estimated by temperature flux modeling 

(Essaid and others, 2008). Finally, a considerable volume of 

deep ground water flows out of the catchment as ground water 

(fig. 3), not discharging to the surface system until it reaches 

Granger Drain or the Yakima River (fig. 1).

Water-level measurements in wells in the northern part of 

the catchment—at sites W24 and W25 (fig. 1)—consistently 

showed a downward gradient (fig. 6B-C). Several lines of 

evidence indicate that a downward vertical gradient also 

exists in the ground-water system near well W30. Although a 

second well at a different depth was not available to confirm 

it, the seasonal fluctuations in the ground-water level and 

temperature at W30 were similar to those in W24 and W25. In 

addition, age tracers (SF6 and CFCs) in water from W30 were 

consistent with concentrations in the atmosphere in the early 

1980s, indicating little mixing of this water with either older 

or younger water. Finally, there are no surface water discharge 

zones in the area. All these factors are consistent with 

predominately downward vertical movement of ground water.

Ground-water levels in the northern part of the catchment 

fluctuated on an annual cycle (fig. 7A-C), with the lowest 

levels occurring in late spring to early summer, and the highest 

levels occurring in late summer to early fall in a delayed 

response to irrigation. The annual range in water levels in 

these wells was 1–2 m. This range is larger than was observed 

downgradient because the relatively thick unsaturated 

zone in the upper catchment prevents discharge to surfacewater outlets. Although the water table rises and falls in the 

upper portion of the catchment in response to infiltrating 

irrigation water, the response to individual irrigation events 

is dampened during the movement of the water through the 

thick unsaturated zone. Water temperatures in these wells 

also fluctuated on an annual cycle, but the seasonal variation 

was less than 1°C (fig. 7A-C), again due to the insulating and 

moderating influence of a relatively thick unsaturated zone. 

In the southern part of the catchment, at sites W20 and 

W21 (fig. 1), as well as at neighboring site W32, groundwater levels showed an upward gradient (fig. 6F-H). At these 

wells, water levels sometimes fluctuated on a daily basis, but 

showed no seasonal pattern (fig. 7D-E). The daily fluctuations 

were likely a response to individual irrigation events and 

Figure 4. Discharge for the DR2 Catchment surface-water outflow (site W13), Yakima River basin, 

Washington.

OR_09_0263_Sprague_McCarthy_Fig04

Sunnyside Canal 

 empty

Sunnyside Canal 

 flowing

0.00

0.05

0.10

0.15

0.20

0.25

0.30

DISCHARGE, IN CUBIC METERS PER SECOND

JAN FEB MAR APR MAY JUNE JULY AUG SEPT OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT OCT

2003 2004

NOV DEC
Effects of Agricultural Practices 7

(or) evapotranspiration, evident in these wells because the 

water table in this part of the catchment is relatively shallow. 

The shallow water table also was reflected in the water 

temperatures in these wells. Relative to those in the upper 

catchment, temperatures varied considerably, with summer 

maximum temperatures approximately 5°C greater than winter 

minimum temperatures (fig. 7).

Site W23 is in the midcatchment, where the predominant 

direction of vertical flow in the ground-water system 

transitions from downward to upward. Comparing levels 

measured in sites W23p and W23q (fig. 8) shows that the 

vertical gradient is generally upward, but periodically reverses 

to downward during the irrigation season. Data from this 

well demonstrate the response of the ground-water system 

to individual irrigation events and illustrate changes in the 

flow system in response to a change in irrigation method. 

Rill irrigation was used near these wells during 2003. In 

2004, the farmland immediately upgradient of these wells 

was converted to sprinkler irrigation. During 2003, the 

frequency of head reversals was greater and the magnitudes of 

downward gradients were greater. Water levels in these wells 

also illustrate the general seasonal effect of irrigation—the 

vertical gradient diminished when canal deliveries ceased in 

mid-October 2003, and approached zero by the end of the 

end of the winter. Finally, corresponding increases in water 

temperature (fig. 8) indicate that gradient reversals in the 

ground water at site W23 are not due simply to a pressure 

response, but rather to warmer water from the surface or near 

surface actually being transported into the saturated zone and 

raising the local water table.

Estimated dates of ground-water recharge, based on 

interpretation of the CFC, SF6, and 3H data (Green and others, 

2008), generally are consistent with the conceptual model of 

subsurface flow developed from ground-water levels (fig. 9). 

Data from wells in the midcatchment (sites W23 and W24) 

suggest that this is a mixing zone of waters recharged at 

different times. Age tracers from site W24q are consistent with 

this water being a mixture of water recharged around 2000 and 

water recharged around 1970. Age-tracer data from site W23q 

are consistent with water in this well being predominantly 

water recharged around 1980 but indicate contributions from 

water recharged prior to the mid-1960s. These mixtures are 

consistent with vertical mixing that would result from periodic 

vertical gradient reversals in the midcatchment and also with 

the conceptual model of a dynamic shallow flow system 

highly influenced by irrigation applications and drainage 

modification sitting atop a reservoir of considerably older, 

slower moving water. Throughout the catchment, water from 

the shallow water-table wells contained at least a component 

of recently recharged water, reflecting the movement of excess 

irrigation water into the underlying saturated zone.

OR_09_0263_McCarthy_Fig05

Evapotranspiration

A

A

E

D

C

E

B B

D

Buried drain Stream

Buried drain

Precipitation

and Irrigation

WATER TABLE

Ground water

discharge to stream

Figure 5. Conceptualization of the hydrology of the DR2 catchment, Yakima River basin, Washington. (Near surface flow paths include 

(A) infiltration and percolation to the water table, (B) infiltration and interception by buried drains, and (C) overland/near-surface flow. 

Ground-water follows (D) shallow, short flow paths and (E) deep, longer flow paths.)
8 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

Figure 6. Water levels in well pairs in the DR2 catchment, Yakima River basin, Washington. (The single well at site W30 is shown 

for comparison purposes only; suffix p indicates the shallowest well at each site; q, r, and s indicate increasingly deeper wells, 

respectively.)

OR_09_0263_McCarthy_Fig06

244.0

244.5

245.0

245.5

246.0

W25p

W25q

239.0

239.5

240.0

240.5

241.0

WATER LEVEL ELEVATION, IN METERS

W24p

W24q

237.0

237.5

238.0

238.5

239.0

W31p

W31q

235.0

235.5

236.0

236.5

237.0

W23p

W23q

230.0

230.5

231.0

231.5

232.0

W32p

W32q

230.0

230.5

231.0

231.5

232.0

W21p

W21q

W21r

W21s

227.0

227.5

228.0

228.5

229.0

W20p

W20q

252.0

252.5

253.0

253.5

254.0

W30p

A M J J A

2003

S O N D J F M A M J

2004

J A S O N D J

2005 2003 2004 2005

A M J J A S O N D J F M A M J J A S O N D J

A.

B.

C.

D.

E.

F.

G.

H.
Effects of Agricultural Practices 9

Figure 7. Water levels and water temperatures in ground water in the DR2 catchment, Yakima River basin, Washington.

Figure 8. Ground-water head gradient (black line) and temperature (grey line) at site W23, DR2 catchment, Yakima River 

basin, Washington. (A positive gradient indicates upward flow.)

Sunnyside Canal empty

Sunnyside Canal flowing

-0.08

-0.04

0.00

0.04

2

6

10

14

0.08 18

GROUND-WATER HEAD GRADIENT

JUNE JULY AUG SEPT

2003

OCT NOV DEC JAN FEB MAR APR MAY JUNE

2004

JULY AUG SEPT OCT NOV

WATER TEMPERATURE, IN DEGREES CELSIUS

GRADIENT

TEMPERATUREOR_09_0263_McCarthy_Fig07

E. W20p

227.0

227.5

228.0

228.5

D. W21p

229.5

230.0

230.5

231.0

F. W23p

235.0

236.0

237.0

238.0

B. W24p

239.5

240.0

240.5

241.0

5

10

15

20

TEMPERATURE , IN DEGREES CELSIUS

Water level

Temperature

A. W25p

244.5

245.0

245.5

246.0

246.5

WATER SURFACE ELEVATION, IN METERS

WATER SURFACE ELEVATION, IN METERS

5

10

15

20

C. W30p

252.0

252.5

253.0

253.5

254.0

5

10

15

20

5

10

15

20

TEMPERATURE , IN DEGREES CELSIUS

5

10

15

20

5

10

15

20

A M J J A

2003

S O N D J F M A M J J A S O N D J

2004 2005

A M J J A

2003

S O N D J F M A M J J A S O N D J

2004 2005
10 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

The effects of artificially enhanced drainage in the 

southern part of this system can be seen by comparing the 

hydrographs of wells at sites W20p and W21p (fig. 7D-E). 

Short-term fluctuations in the water level at W20p show the 

effects of individual irrigation events in the adjacent pasture. 

By contrast, the water level at W21p shows little variation, 

likely due to the damping effect of the shallow drain that 

surrounds this field and efficiently shunts excess irrigation to 

the surface-water system. Age-tracer data from W21p (fig. 9), 

which indicate that the shallow ground water here was not 

recently recharged, support this reasoning. 

The stable isotopes of water from selected sites (fig. 10) 

also corroborate the conceptual model of flow in DR2. From 

late April to late August, the canal water becomes enriched 

in the heavier isotopes, oxygen-18 (18O) and deuterium 

(2H). Samples from W23p and W24p are isotopically 

indistinguishable from late season canal water, consistent with 

this shallow ground water being recently applied irrigation. 

W21s is somewhat more depleted in the heavy isotopes than 

the other wells sampled. This was the deepest and oldest 

ground water sampled (fig. 9), and this isotopic signature 

likely reflects a contribution from older, regional ground 

water. W25p is slightly enriched in the heavier isotopes 

relative to other samples; these isotope values suggest a source 

of water similar to other nearby ground water (such as that 

from W23p, W24p, and W25q) that has undergone additional 

evaporative losses. 

The isotopic composition of streambed water from W63c 

differs considerably from all other water sampled. That sample 

is much more depleted in 2H and 18O than other water samples 

collected for this study, indicating that the shallow subsurface 

water near the catchment outlet is derived from a different 

source than other water sampled. Particle-tracking simulations 

suggest that the deepest, longest ground-water flow paths in 

the catchment discharge near W63c and that water from the 

streambed there includes a significant component of the oldest 

ground water in the catchment. Tritium data (not shown) for 

the three streambed sites sampled (W51c, W55b, and W64c) 

also indicate that water from these sites includes a substantial 

component of relatively old water, recharged more than 50 

years ago.

The isotopic signature of water from the DR2 drain 

(W13) is similar to that of shallow ground water and water 

from the Sunnyside Canal, and the shift in isotopic signature 

from spring to summer in water from the drain mimics that 

seen in water from the canal. During both seasons, however, 

the water from DR2 drain was slightly depleted in the heavier 

isotopes relative to corresponding canal water samples, which 

is consistent with a small contribution from deep ground water 

(fig. 10). 

Figure 9. Estimated ground-water recharge dates in the DR2 catchment, Yakima River basin, Washington. (*Estimated 

recharge date for seven streambed samples—two from the downstream transect and five from the upstream transect; see 

figure 1 for location of section A–A’.)

OR_09_0263_Sprague_McCarthy_Fig09

p 1982

q 1993

q 1980

p 1994

p 1995

s 1946

r 1950

q 1995

q 1953

p 1962

p 2000

p 2003

q 1950

p 2003

Streambed

transects 1950*

Sunnyside

Canal

WATER TABLE

HORIZONTAL COORDINATE, IN METERS

ELEVATION, IN METERS, RELATIVE TO NAVD 1988

200

225

250

275

300

W21

W30

W25

W22 W23

W24

W20

DR 2

A’

A

-500 0 -500 1,000 1,500 2,000 2,500 3,000 3,500 4,000 4,500
Effects of Agricultural Practices 11

Water Chemistry

Water chemistry data were collected at sites representing 

several environmental compartments (fig. 1). Analysis of 

samples from the Sunnyside Canal (W15) indicates the 

composition of imported irrigation water prior to distribution 

in the catchment. Samples from a field drain (W42) provide 

an example of the chemistry of excess irrigation runoff from 

a single field—in this case likely a mixture of overland flow 

and shallow soil drainage. Samples from wells (W20–W32) 

reveal the characteristics of ground water at various locations 

throughout the catchment, both near the water table and 

somewhat deeper, but all in the shallow part of the flow 

system. Sites in two streambed transects in the lower reach of 

DR2 (W51–W65) show the composition of ground water just 

prior to its discharge into the stream. Finally, samples from 

near the DR2 catchment outlet (W13) reveal the composition 

of surface-water discharge from the catchment.

As discussed earlier, virtually all of the surface-water 

discharge from the catchment can be attributed to excess 

irrigation. As this water passes through the catchment, its 

chemistry is altered by biochemical and geochemical reactions 

at the land surface, in the soil, and in the ground-water system.

Fertilizers and other soil amendments used in the DR2 

catchment are important sources of N and P, as well as 

potassium, calcium, magnesium, sodium, chloride, and sulfur. 

Cattle manure is applied as a fertilizer and soil amendment to 

many crops in the area either as liquid slurry or as solids, and, 

based on the classification scheme of Kendall (1998), 15N and 

18O isotopes of nitrate (fig. 11) suggest that manure may be a 

major source of the nitrate measured in waters throughout the 

catchment. 

Mineralogical analyses of subsurface material (sampled 

during well drilling) show its composition is predominantly 

quartz, plagioclase, potassium feldspar, and calcite. Through 

weathering processes, these minerals are abundant sources 

of silica, calcium, sodium, and potassium. Dolomite and 

hornblende, which contain magnesium, also are common in 

the area. Finally, smectite, which has a high cation-exchange 

capacity, was an important component of the colloidal fraction 

of most samples analyzed, and likely plays a role in water 

chemistry.

Comparing the chemistry of water from a number of 

environmental compartments and locations provides insight 

into the processes that affect the quality of water discharging 

from this catchment:

Irrigation water.—Water from the Sunnyside Canal had 

the lowest concentrations of major solutes and dissolved 

nutrients of any compartment sampled (figs. 12–13). Because 

the canal is the major source of water to the catchment, the 

chemistry of water from other environmental compartments 

gives an indication of how this canal water is altered as it 

passes through the catchment.

Figure 10. Abundance of deuterium and oxygen–18 in water samples from the DR2 catchment, Yakima River basin, 

Washington.

OR_09_0263_Sprague_McCarthy_Fig10

W21s

W23p

W24p

W25q

W63c

W25p

W15—04-28-04

W13—8-24-04

W15—08-25-04

W13—2-18 and 4-27-04

GLOBAL METEORIC WATER LINE

-150

-130

-110

-90

-70

-20 -19 -18 -17 -16 -15 -14 -13 -12

δ 18OV-SMOW, PER MILLIMETER

δ DV-SMOW, PER MILLIMETER
12 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

Figure 11. Abundances of oxygen-18 and nitrogen-15 in nitrate in water samples from the DR2 catchment, Yakima River 

basin, Washington.

0

350

700

1,050

1,400 N=6

N=6

N=18 N=12 N=8 N=8 N=8 N=16 N=21 N=30 N=27 N=34

CANAL

(W15)

FIELD DRAIN

(W42)

UPPER BASIN SHALLOW GROUND WATER

(W30P, W25P, W24P)

UPPER BASIN DEEPER GROUND WATER

(W25Q, W24Q)

MID BASIN SHALLOW GROUND WATER

(W31P, W23P)

MID BASIN DEEPER GROUND WATER

(W31Q, W23Q)

LOWER BASIN SHALLOW GROUND WATER

(W32P, W22P, W21P, W20P)

LOWER BASIN DEEPER GROUND WATER

(W32Q, W21Q,R,S, W20Q)

UPSTREAM STREAMBED TRANSECT

(W61A –W65C)

DOWNSTREAM STREAMBED TRANSECT

(W51A –W55C)

BASIN OUTLET

(W13)

SPECIFIC CONDUCTANCE, IN MICROSIEMENS PER CENTIMETER

Outlier

10th percentile

Median

25th percentile

75th percentile

90th percentile

Number of samples

EXPLANATION

Figure 12. Distribution of specific conductance of water samples from the DR2 catchment, Yakima River basin, 

Washington.

OR_09_0263_Sprague_McCarthy_Fig11

Ground water

Stream bed

TYPICAL DENITRIFICATION

TRAJECTORY

-10

-8

-6

-4

-2

0

2

4

6

8

10

12

0 2 4 6 8 10 12 14 16 18 20

δ 15N[NO3

-

]

δ 18O[NO3

-

]
Effects of Agricultural Practices 13

Figure 13. Distribution of concentrations of major solutes in water samples from the DR2 catchment, Yakima River 

basin, Washington. 

OR_09_0263_Sprague_McCarthy_Fig13

0

60

120

180

0

20

40

60

0

20

40

60

0

40

80

120

160

CANAL

(W15)

FIELD DRAIN

(W42)

UPPER BASIN SHALLOW GROUND WATER

(W30P, W25P, W24P)

UPPER BASIN DEEPER GROUND WATER

(W25Q, W24Q)

MID BASIN SHALLOW GROUND WATER

(W31P, W23P)

MID BASIN DEEPER GROUND WATER

(W31Q, W23Q)

LOWER BASIN SHALLOW GROUND WATER

(W32P, W22P, W21P, W20P)

LOWER BASIN DEEPER GROUND WATER

(W32Q, W21Q,R,S, W20Q)

UPSTREAM STREAMBED TRANSECT

(W61A –W65C)

DOWNSTREAM STREAMBED TRANSECT

(W51C –W55C)

BASIN OUTLET

(W13)

CALCIUM, MILLIGRAMS PER LITER CHLORIDE, IN MILLIGRAMS PER LITER SILICA, IN MILLIGRAMS PER LITER AS SiO2 SULFATE, IN MILLIGRAMS PER LITER

N=6 N=18 N=12 N=8 N=8 N=8 N=16 N=21 N=30 N=27 N=34

N=6

Outlier

10th percentile

Median

25th percentile

75th percentile

90th percentile

Number of samples

EXPLANATION
14 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

Field drain.—The field drain flowed year-round, and 

both the discharge and chemical character of the water 

fluctuated with time. During winter, the major solute 

chemistry of water from the drain was similar to that of 

water from nearby well W21p, suggesting that winter flow 

in the drain was discharging ground water. Over the course 

of the irrigation season, the chemistry of the water from the 

field drain varied considerably (for example, N ranges from 

less than 1 to more than 23 mg/L; silica ranges from 13 to 

47 mg/L), suggesting changing contributions from several 

sources, including ground water, shallow soil water, and 

irrigation tailwater. This composite discharge from the drain 

consistently had higher concentrations of major solutes and 

dissolved nutrients than water from the canal (figs. 12–13). 

Concentrations of the major solutes calcium, magnesium, 

potassium, sodium, chloride, sulfate, and silica, were inversely 

related to drain flow rates (R2 = 0.4–0.6). Concentrations of 

nitrate also tended to be lower at higher flow rates (R2 = 0.3), 

but although the highest concentrations of soluble reactive 

P (SRP) were measured during low-flow conditions, there was 

no apparent relationship between SRP and flow (R2 < 0.1). 

The major solutes, as well as nitrate, also were inversely 

correlated with concentrations of suspended sediment in water 

from the field drain, though relationships were weaker than for 

discharge (R2 = 0.2–0.3). The highest concentrations of SRP 

also occurred when concentrations of suspended sediment 

were low, but again, the relationship between SRP and 

suspended sediment was not significant (R2 < 0.1). Data from 

Ebbert and others (2003) and Fuhrer and others (2004) point 

to a relatively constant contribution of SRP from ground water 

in this area. The poor correlation between SRP and suspended 

sediment may reflect differing mixtures of shallow ground 

water, soil water, and overland flow, in which concentrations 

of suspended sediment and dissolved constituents can vary 

considerably, depending on the amount of time since the field 

was last tilled and the timing of sample collection relative to 

individual irrigation events. Longer contact times between soil 

and water at lower flow rates may also be a contributing factor 

to the patterns observed. Durand and others (1999) noted that 

increased depth and velocity of overland flow (such as would 

occur during times of high drain discharge) tended to decrease 

concentrations of solutes.

Ground water.—The chemistry of the water from most 

individual wells varied little over the course of the study, but 

differences in water chemistry among wells were substantial. 

Relative to water from the canal and field drain, ground water 

typically had higher concentrations of major solutes. Although 

concentrations varied considerably among wells, water from 

the shallow wells typically had higher concentrations than that 

from deeper wells, suggesting that water-rock interactions in 

the subsurface may be a less important source of the major 

solutes than near-surface sources such as cattle manure, other 

fertilizers and soil amendments, and weathered soil.

The highest concentrations of N in ground water, 

which was present predominantly as nitrate, generally were 

detected in water from wells in the upper catchment (sites 

W24, W25, and W30). Concentrations of N in water samples 

collected from well W25p consistently exceeded 70 mg/L. 

This is probably the result of a complex interaction of factors, 

including the local ground-water flow system and local 

agricultural practices. Site W25 is at a local topographic 

high, and subsurface flow is likely to be directed downward 

rather than laterally. The very recent recharge date calculated 

for W25p (fig. 9) is consistent with relatively rapid, direct 

downward flow near the water table. Furthermore, this 

well is in an area where cattle manure, a potential source of 

considerable N, was applied liberally.

Concentrations of excess dissolved N2 in water from 

most wells was low (table 1). Dissolved N2 in excess of 

the concentration achieved through equilibration with the 

atmosphere plus excess air (Dunkle and others, 1993) indicates 

that nitrate previously present in the water has undergone 

denitrification—the process by which nitrate is transformed 

into N2. Thus, low concentrations of excess dissolved N2 in 

water from most wells indicate that denitrification is not a 

major process in this ground-water system. Green and others 

(2008) present the details of excess dissolved N2 calculations 

and discuss the limited denitrification in this ground-water 

system.

Streambed transects.—Similar to the findings for ground 

water, the chemistry of water from individual sites within the 

streambed transects varied little over the course of the study. 

However, the range in the data from each transect (figs. 1, 

11–14, table 1) shows that water chemistry differs over very 

small distances (tens of centimeters) in this system. Some 

of these differences may result from spatial variations in the 

composition of the streambed, but the variability observed 

also suggests that flow paths from different source areas are 

converging to discharge into this lower reach of DR2, and 

provides insight into differences between the chemistry of 

relatively deep ground water that discharges upward into the 

stream and that of the shallow ground-water system that flows 

laterally into the stream. 

Compared to the ground water sampled, water from 

both streambed transects tended to have lower specific 

conductance and alkalinity, as well as lower concentrations 

of calcium, magnesium, and sodium (fig. 12). In contrast, 

concentrations of potassium, chloride, silica, and SRP tended 

to be similar to those measured in ground water (figs. 12–13). 

These conditions indicate that differences between water in 

the streambed and ground water were not likely due to simple 

geochemical processing or dilution (from unapplied irrigation 

water, for example), but suggests that a component of the 

streambed water comes from a source distinct from other 

ground water sampled. We hypothesize that this source is 

relatively old ground water discharging from the deep, long 

ground-water flow paths mentioned previously.
Effects of Agricultural Practices 15

The concentrations of nitrate were lower in water from 

the streambed than in most ground water sampled (fig. 14). 

In water samples collected from the upstream transect, 

concentrations of excess N2 consistently exceeded 2.5 mg/L, 

except at sites W62b and W61b (table 1). In water samples 

collected from the downstream transect, concentrations of 

excess N2 ranged from less than 1 to more than 6 mg/L (at 

Table 1. Excess nitrogen gas (N2) measured in the DR2 

catchment, Yakima River basin, Washington.

[Site locations are shown in figure 1. Suffix p indicates the shallowest well at 

each site; q, r, and s indicate increasingly deeper wells, respectively] 

site W54a). These data indicate that denitrification occurs in 

portions of the subsurface, but that conditions vary over very 

small distances. Values of 18O and 15N isotopes from nitrate 

collected from the streambed also suggest that denitrification 

occurs in this zone (fig. 11). (Puckett and others [2008] 

provide further details on denitrification in the streambed.) 

Although several lines of evidence indicate that denitrification 

occurs in this zone, the effects on nitrate concentrations in 

surface water are limited by the small flux of water involved. 

Several factors combine to constrain water flux through the 

streambed. First, as mentioned earlier, the permeability of the 

streambed is low; second, irrigation flow during the growing 

season raises the water level in DR2, which reduces the 

gradient from ground water to the stream; and third, enhanced 

shallow drainage throughout the catchment shunts ground 

water laterally toward surface drains and effectively bypasses 

deeper flow paths.

Conditions at sites W61b and W62b, in the shallow, 

western part of the upstream transect indicate that lateral 

flow to the stream from a distinct water source occurs in this 

area. Concentrations of nitrate here were higher than in the 

rest of the transect, but concentrations of excess N2 were 

somewhat lower, suggesting a source of nitrate-rich water, 

but only limited progression of denitrification (due to either 

reduced capacity or shorter residence time). These two sites 

also had higher specific conductance, alkalinity, calcium, 

magnesium, potassium, sodium, and total N (mostly present 

as nitrate), and lower concentrations of chloride relative to 

other sites in the transect. Furthermore, water temperature 

near these sites was periodically colder than water deeper 

in the streambed (sites W61c and W62c) or water near the 

bottom of the overlying stream (fig. 15). These data indicate 

that colder water was flowing laterally toward the transect at 

middepth and provide evidence of lateral ground-water flow 

to the stream.

Catchment outlet.—The chemistry of the water at the 

catchment outlet is consistent with the water being a mixture 

of canal water, field drainage, ground water, and streambed 

discharge. Examining the chemistry at the catchment outlet 

in the context of the annual streamflow hydrograph provides 

further insight into processes in the catchment. Several of the 

major solutes (calcium, magnesium, sodium, chloride, sulfate, 

and silica) were inversely related to stream discharge. This 

pattern of lower concentrations during the irrigation season, 

when the highest discharges occurred in DR2, is illustrated by 

calcium and silica data (fig. 16A, B). Concentrations of nitrate 

in water from DR2 also were highest during the nonirrigation 

season, but concentrations during the irrigation season varied 

more than those of the major solutes (fig. 16C). In contrast, 

concentrations of SRP in the catchment outflow were highly 

variable, but generally increased during the irrigation season 

(fig. 16D).

Site

identification 

No.

Concentration

(milligrams per liter) Number

of 

samples Average Minimum Maximum

Ground water

W20p 0.00 0.00 0.00 4

W20q 2.93 2.84 3.00 4

W21p 0.24 0.00 0.50 4

W21q 0.00 0.00 0.00 4

W21r 0.43 0.00 0.87 4

W21s 0.18 0.00 0.38 4

W23p 0.86 0.13 1.60 4

W23q 2.03 0.90 3.10 4

W24p 0.29 0.22 0.36 2

W24q 0.02 0.00 0.04 2

W25p 0.35 0.25 0.45 2

W25q 0.88 0.86 0.89 2

W30p 0.69 0.42 0.94 4

W31p 2.14 1.96 2.32 4

W31q 0.00 0.00 0.00 4

W32p 1.57 1.50 1.64 2

W32q 0.00 0.00 0.00 4

Upstream streambed transect

W61b 1.79 1.78 1.80 2

W61c 2.84 2.80 2.88 2

W62b 2.13 2.11 2.14 2

W62c 3.19 3.18 3.20 2

W63a 2.89 2.80 2.98 2

W63c 2.93 2.89 2.97 2

W64a 2.73 2.64 2.81 2

W64c 3.25 3.17 3.34 2

 Downstream streambed transect

W51a 0.7 0.64 0.79 2

W51c 1.7 1.61 1.79 2

W52b 0.9 0.92 0.92 1

W53b 1.4 1.31 1.47 2

W54a 6.5 6.25 6.76 4

W55b 1.0 0.90 1.02 2
16 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

Figure 15. Vertical temperature profile measured in the streambed in the DR2 catchment, Yakima River basin, Washington, 

September 2004. OR_09_0263_Sprague_McCarthy_Fig14 CANAL (W15) FIELD DRAIN (W42) UPPER BASIN SHALLOW GROUND WATER

(W30P, W25P, W24P)

UPPER BASIN DEEPER GROUND WATER

(W25Q, W24Q)

MID BASIN SHALLOW GROUND WATER

(W31P, W23P)

MID BASIN DEEPER GROUND WATER

(W31Q, W23Q)

LOWER BASIN SHALLOW GROUND WATER

(W32P, W22P, W21P, W20P)

LOWER BASIN DEEPER GROUND WATER

(W32Q, W21Q,R,S, W20Q)

UPSTREAM STREAMBED TRANSECT

(W61A –W65C)

DOWNSTREAM STREAMBED TRANSECT

(W51C –W55C)

BASIN OUTLET

(W13)

N=6 N=18 N=12 N=8 N=8 N=8 N=16 N=21 N=30 N=27 N=34

0.01

0.1

1

10

100

1,000

NITRATE, IN MILLIGRAMS PER LITER AS N

0.001

0.01

0.1

1

SOLUBLE REACTIVE PHOSPHORUS,

IN MILLIGRAMS PER LITER AS P

N=6

Outlier

10th percentile

Median

25th percentile

75th percentile

90th percentile

Number of samples

EXPLANATION

Figure 14. Distribution of concentrations of nitrate and soluble reactive phosphorus in water samples from the DR2 

catchment, Yakima River basin, Washington.

Stream bottom

W 62b

W 62c

13

14

15

16

17

15 16 17 18 19

SEPTEMBER 2004 

20 21 22 23

TEMPERATURE, IN DEGREES CELSIUS
Effects of Agricultural Practices 17

Figure 16. Concentrations of selected solutes (square symbols) and stream discharge (solid line) at the DR2 catchment 

outflow (site W13), Yakima River basin, Washington.

OR_09_0263_McCarthy_Fig16

0

10

20

30

40

50

60

SILICA, IN MILLIGRAMS PER LITER 

AS SiO2

0

0.1

0.2

0.3

0

10

20

30

40

50

60

70

80

90

CALCIUM, IN MILLIGRAMS PER LITER

0

0.1

0.2

0.3

0

1

2

3

4

5

6

7

NITRATE, MILLIGRAMS PER LITER AS N

DISCHARGE, IN CUBIC METERS PER SECOND

0

0.1

0.2

0.3

0

0.1

0.2

0.3

0.4

0.5

SOLUBLE REACTIVE PHOSPHORUS,

IN MILLIGRAMS PER LITER AS P

0

0.1

0.2

0.3

2003 2004 2005

SEPT OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEP OCT NOV DEC JAN

Sunnyside Canal empty

Sunnyside Canal flowing

A

B

C

D
18 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

Inverse End-Member Mixing Analysis

An inverse application of a simple end-member mixing 

analysis (EMMA) was used to help understand the differences 

in water chemistry between irrigation season and base-flow 

conditions in DR2 and to gain insight into the transport of 

agricultural chemicals in the catchment. As discussed in the 

previous sections, flow in DR2 was more than twice as high 

during the irrigation season than during base-flow conditions 

(in the winter), and the concentrations of most solutes were 

diluted during the higher-flow period. Of the major solutes and 

nutrients, only concentrations of SRP were higher during the 

irrigation season. 

Conceptually, the water in DR2 during the irrigation 

season can be described as a mixture of ground-water base 

flow and a seasonal component, referred to here as “seasonal 

agricultural flow” (SAF). This conceptualization, modified 

from Domagalski and others (2008), can be expressed 

mathematically as

2

2

,

where

is the median total discharge in DR2

during the irrigation season,

is ground-water base flow to the stream

during the irrigation season, and

is SAF.

i bf SAF i DR

i DR

i bf

SAF

Q Q Q

Q

Q

Q

− −

−

−

= + (1)

Comparing and contrasting the chemical characteristics of the 

hypothetical SAF with those of canal water gives insight into 

the composite effects of agriculture in the DR2 catchment on 

water quality.

For a conservative solute, the mass balance can be 

expressed as

2 ( ) ( ) ( ) , QC i D− R QC i−bf QC SAF = + (2)

where Ci-DR2, Ci-bf, and CSAF are the median irrigation season 

concentrations of the solute in DR2, ground-water base flow, 

and SAF, respectively. Combining equations 1 and 2 and 

solving for CSAF yields

2

2

( ) ( ) , i DR i bf

SAF

i DR i bf

QC QC C

Q Q

− −

− −

− = − (3)

To solve this equation for individual solutes, the median 

discharge and concentrations of solutes measured at site W13 

between mid-June and mid-September 2004 were used to 

approximate Qi-DR2 and Ci-DR2 . Hydraulic head data collected 

in the stream and in nearby ground water (fig. 7) showed that 

the average hydraulic gradient from ground water toward 

DR2 during the irrigation season was only about 80 percent 

of the gradient measured during the nonirrigation season. On 

the basis of these data, Qi-bf was approximated as 80 percent 

of the median discharge measured at site W13 during the 

nonirrigation season, from mid-October 2003 through 

mid-March 2004. Finally, making the assumption that the 

concentrations of solutes in base flow were similar during the 

irrigation and nonirrigation seasons, the medians of solute 

concentrations measured at site W13 between mid-October 

2003 and mid-March 2004 were used to approximate Ci-bf .

The composition of SAF (table 2), calculated on the 

basis of equation 3, serves as a tool for understanding source 

and transport processes in the DR2 catchment. Conceptually, 

SAF is a hypothetical composite of excess irrigation water 

and includes system spill (water that is transported directly 

from the irrigation delivery system to the surface-drainage 

system, without being released to the landscape), tailwater, 

overland flow, and applied irrigation water that infiltrates and 

then travels by way of shallow, short subsurface flow paths 

(subsurface drains, for example) to the surface-water system 

without being incorporated into the ground-water system. 

SAF is, therefore, water from the canal delivery system that 

passes through the catchment into DR2 during a single growing 

season. Comparison of the chemical characteristics of this 

hypothetical water to those of canal water provides insight into 

the net composite effect of current agriculture on water quality 

in the DR2 catchment. Furthermore, because nearly all groundwater base flow in the catchment can be attributed to irrigation 

over the past century (Payne and others, 2007), differences 

between SAF and base flow are attributable to changes that 

result from passage through the subsurface and (or) changes in 

agricultural practices over time. Finally, a comparison of SAF 

characteristics to those of water from the field drain enables a 

further understanding of how closely the net effect of processes 

in the single field sampled approximates the net effect of 

processes in the catchment as a whole.

SAF compared to canal water and base flow.—

Calculated concentrations of most solutes in the hypothetical 

SAF were intermediate between concentrations measured 

in water from the canal and those measured in water from 

DR2 during base-flow conditions (table 2). For several 

major solutes (calcium, magnesium, potassium, sodium, and 

silica), concentrations calculated for SAF were two to four 

times greater than concentrations in canal water, but only 

about 40–50 percent of the concentrations measured in base 

flow samples (fig. 17). These differences suggest that excess 

irrigation water picks up a considerable load of solutes as 

it travels through the catchment, even when following the 

relatively rapid surface and near-surface transport pathways 

postulated for SAF. However, subsurface flow paths that 

discharge as base flow are responsible for the greatest 
Effects of Agricultural Practices 19

contribution of solutes to DR2. Estimates of recharge dates 

for the ground water sampled (fig. 9) indicate that time spent 

in the subsurface is on the order of several years to several 

decades. Therefore, in addition to chemical changes in the 

water that result from its passage through the subsurface, some 

of the differences between SAF and base flow may be the 

result of changes in agricultural practices over the past several 

decades.

In contrast to the major solutes, the calculated 

concentration of nitrate in SAF was nearly an order of 

magnitude greater than the median concentration measured in 

canal water (fig. 17A), but only about 30 percent of the median 

concentration measured in base flow. The SRP concentration 

in SAF was more than six times greater than the median 

measured in canal water (fig. 17D), and twice the median 

concentration measured in base flow.

SAF compared to field drain discharge.—SAF 

concentrations calculated for most of the major solutes, as well 

as nitrate, were similar to the median concentrations measured 

in water from the field drain (W42). This similarity indicates 

that with respect to most major solutes (calcium, magnesium, 

potassium, sodium, and silica), the net effect of sources and 

transport processes in the field from which drainage was 

sampled was similar to the net effect of sources and processes 

throughout the catchment as a whole. At both the field scale 

and the catchment scale, soil-water interaction and dissolution 

of applied fertilizers and soil amendments probably accounted 

for virtually all of these solutes. 

In contrast to the major solutes mentioned above, 

concentrations of SRP, chloride, and sulfate were dissimilar in 

SAF and the field drain. Concentrations of SRP, chloride, and 

sulfate calculated for SAF were approximately two times the 

median concentrations measured in water from the field drain. 

These differences indicate that the sources of these solutes 

and (or) the processes affecting their transport and fate in the 

catchment as a whole are not closely approximated by sources 

and processes governing water quality at site W42. 

Given the inherently complex, highly variable nature 

of field-scale runoff processes (Durand and others 1999; 

Langlois and Mehuys, 2003; Cerdan and others, 2004; 

Kurz and others, 2005), the variety of cropping, irrigation, 

tillage, and drainage practices used across DR2, and ongoing 

nearstream and instream biochemical processes, even the 

concentrations of SRP, chloride, and sulfate calculated for 

SAF are remarkably similar to the median concentrations 

measured in water from the field drain. 

Table 2. Composition of surface flow-system components during the irrigation season in the DR2 catchment, Yakima River basin, 

Washington.

[Catchment surface-water outflow: median concentrations measured in DR2 (site W13) from mid-June through mid-September 2004. Base flow: median 

concentrations measured in DR2 site (W13) from mid-October 2003 through mid-March 2004. Canal: median concentrations measured in Sunnyside Canal 

(site W15) from mid-June through mid-September 2004. Field drain: median concentrations measured in the field drain (site W42) from mid-June through midSeptember 2004. SAF: hypothetical SAF calculated using equation 3. Abbreviations: SAF, seasonal agricultural flow; SiO2

, silicon dioxide; m3/s, cubic meter 

per second; μS/cm, microsiemen per centimeter; mg/L, milligram per liter; na, not applicable]

Units

Catchment 

surface-water 

outflow

Base flow Canal Field drain SAF

Discharge m3/s 0.204 10.068 na na 0.136

Specific conductance μS/cm 434 657 104 212 321

Nitrate mg/L as N 3.3 5.4 0.22 2.4 2.3

SRP mg/L as P 0.18 0.092 0.029 0.10 0.22

Calcium mg/L 41 64 11 20 29

Magnesium mg/L 14 25 4.2 5.9 9.2

Potassium mg/L 5.4 6.7 1.1 3.3 4.7

Sodium mg/L 25 41 4.7 12 17

Chloride mg/L 11 17 2.1 3.4 7.1

Sulfate mg/L 34 68 3.1 7.6 17

Silica mg/L as SiO2 30 46 14 19 22

1

 Median discharge measured in DR2 (site W13) from mid-October 2003 through mid-March 2004, adjusted by the ratio of nonirrigation-to-irrigation season 

hydraulic gradient from ground water to surface water.
20 Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington

Figure 17. Distribution of concentrations of selected solutes measured in the DR2 catchment outflow components, and 

concentrations calculated for hypothetical seasonal agricultural flow (SAF), Yakima River basin, Washington. 

OR_09_0263_McCarthy_Fig17 NITRATE, MILLIGRAMS PER LITER AS N CALCIUM, IN MILLIGRAMS PER LITER SULFATE, IN MILLIGRAMS PER LITER

SOLUBLE REACTIVE PHOSPHATE,

IN MILLIGRAMS PER LITER AS P CHLORIDE, IN MILLIGRAMS PER LITER SILICA, IN MILLIGRAMS PER LITER AS SiO2

CANAL FIELD

DRAIN

N=4 N=11 N=14

N=5 N=11 N=14

N=7 N=1 N=4 N=11 N=14 N=7 N=1

N=7 N=1

N=5 N=11 N=14 N=7 N=1

N=5 N=11 N=14 N=7 N=1

N=5 N=11 N=14 N=7 N=1

BASE

FLOW

CATCHMENT

OUTFLOW

SAF CANAL FIELD

DRAIN

BASE

FLOW

CATCHMENT

OUTFLOW

SAF

0

20

40

60

80

100

0

20

40

60

80

0

2

4

6

8

0

5

10

15

20

25

0.0

0.1

0.2

0.3

0.4

0.5

0

10

20

30

40

50

N=4

Outlier

10th percentile

Median

25th percentile

75th percentile

90th percentile

Number of samples

EXPLANATION
References Cited 21

Summary and Conclusions

Hydrologic and water-chemistry data from several 

environmental compartments were used to develop an 

understanding of water flow and solute transport in a small, 

irrigated agricultural catchment. An inverse end-member 

mixing analysis then was used to gain a fuller understanding 

of solute sources and transport in the catchment. Considering 

the variation in crops and irrigation methods both across 

the catchment and over time, this approach indicates that 

during the study period, the net effect of processes in the 

catchment as a whole produced similar concentrations of 

most major solutes as the net effect of processes in the single 

field from which drainage was sampled. Data from two 

sampling transects in the streambed provided evidence that 

ground-water flow from different source areas converges 

to discharge to the surface near the catchment outlet, and 

provided insight into differences between the chemistry of 

relatively deep ground water that discharges upward into the 

stream and that of shallow ground water that flows laterally 

into the stream. 

This work indicates that combining irrigation and 

artificial-drainage networks may exacerbate the ecological 

effects of agricultural runoff by increasing direct connectivity 

between fields and streams and minimizing potentially 

mitigating effects of longer subsurface pathways such as 

denitrification and dilution.

Acknowledgments

This work was conducted as part of the USGS National 

Water Quality Assessment Program, and many individuals 

contributed to its success. 

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McCarthy and Johnson—Effect of Agricultural Practices on Hydrology and Water Chemistry, Yakima River Basin, Washington—Scientific Investigations Report 2009–5030