FY 2004 Annual Report for Water Quality and Management National Program 201 

Introduction

Water quantity and quality issues have increasingly become the focus of attention of United 

States citizens, private and public organizations, and units of government striving to meet 

competing demands while protecting the environment and public health. Sound agricultural 

management practices are required to ensure success in maintaining a healthy and productive 

land and water base that sustains local communities, food and fiber production, and also protects 

and restores critical natural systems. Research in this National Program addresses three 

component problem areas: (1) agricultural watershed management; (2) irrigation and drainage 

management; and (3) water quality protection and management. The purpose of the Water 

Quality and Management National Program is to provide practical tools and techniques to meet 

the needs of farmers, ranchers, and other entities involved in controlling, assessing, regulating, 

and managing water resources. 

ARS in cooperation with the Natural Resources Conservation Service (NRCS), Cooperative 

Research Extension and Education Service, USDA Office of Risk Assessment and Cost Benefit 

Analysis, Environmental Protection and other Federal and State agencies have developed a 

watershed assessment program and a national assessment effort. This program is the 

Conservation Effects Assessment Project (CEAP). The purpose of CEAP is to provide the 

farming community, the conservation community, the general public, the Office of Management 

and Budget, legislators, and others involved with environmental policy issues an accounting of 

the environmental effects or benefits obtained from USDA conservation program expenditures. 

The centerpiece of the watershed assessment program is the ARS "benchmark" watersheds. The 

term benchmark is used to distinguish the ARS watersheds from other watersheds where 

watershed assessment research is being initiated under CEAP. Also, the concept of benchmark 

watersheds is used to differentiate the larger scale ARS watersheds from field scale ARS 

research activity. ARS has 60 scientists at nine locations contributing to the research activity on 

12-benchmark watersheds. The location are: Ames, IA, Tifton, GA, El Reno, OK, Temple, TX, 

Oxford, MS, University Park, PA, Columbia, MO, West Lafayette, IN, and Columbus, OH. The 

12-benchmark watersheds represent primarily rain-fed or non-irrigated cropland. In addition to 

these locations, ARS scientists from Ft. Collins, CO, are coordinating a portion of the modeling 

activities. 

The research assessments on the ARS benchmark watersheds are intended to determine an 

optimal selection and placement of conservation management practices to achieve specific water 

quality and other environmental goals, as well as provide initial information important to 

assessing the economic and social factors that facilitate or impede implementation of these 

conservation practices. ARS is developing plans to partner with Economic Research Service, 

NRCS, and several universities to enhance the economic and social science efforts within the 

CEAP program. An ARS research plan for the 12-benchmark watersheds has been peer 

reviewed and is being implemented in 2005 as the first national watershed project aimed at 

quantifying improvements in water derived from implementing economically feasible 

conservation practices. The first report from this effort is scheduled in late 2006. 
In 2004, the Agricultural Drainage Management Systems (ADMS) Task Force was fully 

implemented by ARS, NRCS, and CSREES in cooperation with land improvement contractors, 

drainage industry representatives, private consultants, and farm organizations in seven 

Midwestern States of Iowa, Illinois, Indiana, Minnesota, Missouri, Ohio, and Wisconsin. The 

new era for agricultural drainage is based on removing a minimal amount of excess surface water 

and managing shallow water tables to achieve an optimal mix of economic and social benefits 

while safeguarding key ecological functions. The initial focus has been highly successful where, 

under the lead of ARS, NRCS and State Agriculture Extension Engineers working with farmers 

and cooperators, have rapidly begun to install controlled drainage systems on existing and new 

surface and subsurface drainage systems. Numerous workshops/meetings were held in 2004 and 

many more workshops and conferences are being planned for 2005. The ADMS Task Force has 

been designated as the first technical working group for the ARS, NRCS, CSREES Partnership 

Management Team, where a charter, action plan, flyers, posters, and several technical documents 

have been implemented. Numerous educational brochures and handouts have been developed 

and distributed to the public via two specialty conferences in 2004. 

International activities have also been expanded in FY 2004. Five cooperative projects related to 

soil erosion by water and wind, were developed with the U.S.-China Center for Soil and Water 

Conservation and Environmental Protection. This center is located on the campus of the 

Northwest Sci-Tech University of Agriculture and Forestry (NWSUAF) in Yangling, China. The 

U.S. counterpart is located at the Colorado State University, Fort Collins, Colorado. In 

November of 2004 ARS scientists from West Lafayette, Indiana traveled to Yangling, China to 

provide a 2-week workshop on how to use the Water Erosion Prediction Project model. In 2005 

ARS scientists will be traveling to Yangling to provide training in the use of the Revised 

Universal Soil Loss Equation model, the Wind Erosion Prediction System model, and other 

technology. Chinese scientists are helping ARS scientists design state-of-the art gully erosion 

experiments that will be conducted in China. Results from these experiments will be then 

integrated into the ARS models for use in the United States as well as China. 

Irrigation Management Systems (IMS) project has been developed by three ARS locations in 

cooperation with partners from Israel, the Palestinian Territory, and Jordan. A successful IMS 

Workshop was held in Jordan with full participation from Middle East partners. Funding for the 

multi-location Middle East project has been provided by the U.S. Department of State. In 

addition, the U.S. Department of State is funding a series of projects with Pakistan to share 

technology on water quality and management practices in arid and semi-arid landscapes. The 

projects range from development of efficient irrigation systems to revegetation of drastically 

disturbed native rangelands to control upland erosion and sedimentation of vital flood control 

and water supply structures. 

Selected Accomplishments from the Water Quality and Management national program. 

SWAT is being used worldwide to assess environmental impact. SWAT, which stands for Soil 

and Water Assessment Tool, was developed over the past 30 years by a team of ARS researchers 

at Temple, Texas, in cooperation with other ARS scientists in Bushland, TX, El Reno, OK, 

Tucson, AZ, Ft. Collins, CO, Miami, FL, Ames, IA, and Tifton, GA. Over the past 4 years, the 
U.S. Environmental Protection Agency and ARS have made SWAT available to State agencies 

and consultants throughout the nation to evaluate and assess water quality impairments and to 

assist in developing watershed plans for addressing specific problems. The Natural Resources 

Conservation Service used the SWAT model in its 1997 Resource Conservation Appraisal, in 

which the first national assessment of agricultural water use, tillage systems and fertilizer 

management was made. In 2004, NRCS and ARS are again using SWAT to work together to 

quantify the environmental benefits of conservation practices at the national scale and the 

watershed scale for the Conservation Effects Assessment Project (CEAP). The newest version of 

SWAT has been distributed to hundreds of scientists and engineers at universities, government 

agencies, and consulting firms throughout the world and several international training 

conferences have been held over the past 2 years. 

Management of nitrogen improved to sustain water quality. Proper management of nitrogen in 

agricultural systems while understanding its transport and transformations is becoming 

increasingly important to agricultural producers and to modern society. ARS scientists 

developed a book that included the Nitrate Leaching and Economic Analysis Package (NLEAP) 

computer model developed earlier by ARS. Since their release, both the book and the NLEAP 

model have been used Worldwide. ARS scientists continue to update the model in response to 

user requests to address special situations or unique applications. An updated version of the 

NLEAP model has been delivered to the Natural Resources Conservation Service (NRCS) and 

can be downloaded from NRCS web site. 

Adoption and use of the phosphorus (P) index is widespread. In response to mounting water 

quality concerns, many states have developed guidelines for land application of phosphorus (P) 

based on the potential for P loss in agricultural runoff. These actions have been spurred, in part, 

by a federal initiative in which the U.S. Environmental Protection Agency and USDA created a 

joint strategy to implement Comprehensive Nutrient Management Plans (CNMPs) on Animal 

Feeding Operations by 2008, which considers both agronomic and environmental impacts of 

applied P. To address this need, ARS led the development and refinement of a P Index to rank 

the vulnerability of fields to P loss in runoff and identify those at greatest risk for loss. The 

Natural Resource Conservation Service (NRCS) has adopted the use of the P index in 47 States 

as the basis for development of CMNPs, and over 2000 NRCS field agents and nutrient 

management consultants across the U.S. have received training. Widespread adoption and use of 

the P Index is resulting in the first significant reduction in the threat to water quality from 

nonpoint sources of P. Economic benefits of using this approach are estimated at $204 to $355 

million and include increased recreational use of waters, better shellfish harvest, fewer fish kills, 

lower drinking water treatment costs, and reduced loss of livestock to disease. 

Critical sources of nutrients exported from watershed are delineated. In the northeastern U.S., 

agricultural runoff is a major source of N and P input to waters such as Lake Champlain, Lake 

Erie, and Chesapeake Bay, which are impaired by eutrophication and associated harmful algal 

blooms. To remediate these and other waters around the world, environmental action agencies 

have moved from trying to treat impaired waters to identifying and controlling nutrient sources 

within contributing watersheds. ARS scientists conducted multi-scale, watershed-based studies 

of key chemical and hydrologic factors controlling P and N export from agricultural watersheds 

to locate where they originate on the landscape and enable appropriate remedial measures to be 
targeted to their critical source areas. It was found that most of the P exported (>80%) from 

agricultural watersheds in PA, NY, and MD came from only a small area of the watershed 

(<20%) during a few, rapid storm events. Because most of the P exported predictably occurs 

during short periods and from critical source areas within the much larger watershed, 

remediation can be targeted to these times and areas. In contrast to P, N was exported from most 

of the watershed area and depending on the groundwater flow pathways, can take up to 20 years 

to flow from a field to river channel. These results show the need for site-specific management 

strategies for P and N to account for these spatial and temporal differences in export controls. 

The critical source area concept of nutrient management at landscape and watershed scales is 

more technically defensible, quantitative, and site-specific than previous guidelines. Action 

agencies (NRCS and EPA) and nutrient management divisions of the livestock industry are using 

tools based on these concepts to more reliably evaluate the environmental effects of current and 

proposed agricultural practices at both regional and national levels and to provide management 

recommendations that support a productive and profitable agriculture, while minimizing water 

quality impairment. 

Salinity assessment technology is widely adopted. Soil salinization is a major problem, causing 

decreased crop production and water quality problems, in irrigated lands of arid and semiarid 

regions of the world including the southwestern U.S. Over the past 15 years, ARS researchers at 

Riverside, CA, have developed technology for using electrical resistivity and electromagnetic 

induction sensors (EM) to measure soil salinity. Within the past 4 years, this technology was 

combined into a mobile platform (typically a modified spray tractor) with global positioning 

systems (GPS) and a computer to rapidly and remotely collect soil conductivity data with depth 

and spatially across a field. In cooperation with the U.S. Bureau of Reclamation, a salinity 

assessment network has been recently deployed throughout the Lower Colorado Region. The 

primary end-users of this technology include technical specialists from the U.S. Bureau of 

Reclamation and the Natural Resource Conservation Service along with water district personnel 

throughout the western U.S., various university extension specialists and research scientists in 

saline regions throughout the world, including Canada, Mexico, South America, Australia and 

the Middle East. 

Phyto-remediation of selenium affected soils. Given the scarcity of irrigation water and the lack 

of drainage water disposal facilities, drain water recycling is being used on nearly 200000 ha of 

irrigated California soils and has resulted in an accumulation of selenium (Se) in the soils. The 

continued discharge of subsurface drainage water containing toxic elements such as Se and 

boron (B) will eventually result in the degradation of the environment and agro-ecosystem, and 

could lead to another disaster like that observed at the Kesterson National Wildlife Refuge in the 

mid-1980’s. To prevent a disaster of this magnitude from reoccurring, ARS scientists in 

California have developed a plant-based management approach, defined as phyto-remediation 

that utilizes salt/B tolerant crops, e.g., canola, sunflower, salt and cordgrasss, and even transgenic 

mustard, to extract and volatilize Se when planted on the water- reused soils / drainage sediment. 

This technique has been used successfully at Red Rock Ranch (20 ha), Panoche Drainage 

District (50 ha), and Broadview Water District (3 ha). They determined that canola, as the best 

short-term performer, extracted and volatilized up to 40 % of the Se applied via drainage water 

between 0-30 cm depths. Over multiple years of drainage water reuse, the perennial and lowermaintenance salt and cordgrasses tolerated the elevated soil salt and B levels more effectively 
than the annual crops, and removed at least 20% more Se from 0-90 cm depths than did the 

annual crops. Developing usable products from the crops used for removing Se, e.g., Se-enriched 

animal forage, biofuel, will encourage widespread usage of phytoremediation for susceptible 

regions in the western USA. 

Fertigation can be used efficiently for all irrigation methods. Fertigation brings both nutrients 

and water to plants and at the same time saves money by combining two tasks into an efficient 

system. ARS scientists at three locations have found different ways to improve the application 

of fertilizer and at the same time apply water more efficiently for the three irrigation methods. 

Researchers from Phoenix, AZ found that improved fertilizer mixing and injection procedures 

can be used to improve the uniformity of the fertilizer applications. Scientists at Lincoln, NE, 

working with industry cooperators, developed a new electronic sensor that can be placed at 

different spacing atop a center-pivot irrigation system to apply variable rate fertilizer and water 

applications for precision farming. This same sensor can be used on a high-clearance sprayer or 

other types of farm implements to precisely and accurately apply variable rate fertilizer 

applications on both irrigated and nonirrigated (rainfed) croplands. Also, researchers at Parlier, 

CA, have demonstrated that applying both fertilizers and water on nearly a continuous basis 

through drip irrigations, which are buried underground, can prevent seepage of excess nutrients 

into ground waters. Although uniformity of the fertilizer applications can be higher for sprinkler 

and drip irrigation methods, fertigation can be within 10 to 15 percent for furrow irrigation 

practices. Current estimates are that various fertigation techniques will be used on 50 percent of 

the irrigated lands in the U.S. by 2010 for an additional increase in farm profits of at least $600 

million dollars per year based on conservative estimates for fertilizer savings and increased 

yields alone with consideration given to environmental benefits. 

Grazing cattle on lands where the groundwater was once polluted. ARS scientists in Coshocton, 

OH, recently concluded that cattle could be grazed on pastures that overlie these contaminated 

aquifers without fear of additional contamination from the nitrogen in cattle waste. The secret is 

to minimize or eliminate nitrogen fertilization on the pastures for several years before resuming 

cattle grazing to allow the system to come back into equilibrium. After two years without 

grazing, the ARS scientists found that the nitrate-nitrogen in groundwater was brought down 

from a high of 26 parts per million (ppm) to 2 to 4 ppm without any impact on livestock health or 

performance under both management practices, and the lack of fertilizer caused only a slight 

decrease in grass production. The U.S. Environmental Protection Agency guidelines for human 

drinking water stipulate 10 ppm as the maximum allowable safe level for nitrate-nitrogen. This 

is a nice finding, because it doesn't force farmers to remove cattle permanently from problem 

fields, as long as they first lower the nitrogen levels in the soil and then stop fertilizing the 

pastures at excessive levels once the cattle are again allowed on the land. Hopefully, the 

livestock producer owns additional land or is able to lease land for the cattle for the period of 

time needed to reduce previous levels of contamination to the aquifer. 

Sediment is the nation’s number one pollutant in our streams. ARS scientists in Oxford, MS have 

developed a low-cost means of reducing gully and streambank erosion, one of the major causes 

of soil loss and sedimentation within our nation’s streams. Traditional measures for controlling 

this type of erosion require costly stone or concrete structures. The large woody debris 

structures, being studied by ARS scientists, provide shelter for fish and insects, restores riparian 
habitats, and costs less than traditional methods. The structures consist of uprooted trees stacked 

in crossing layers and are anchored with steel cables to the streambed. The structures reduce 

sediment transport, triggering natural deposition to heal channels enlarged by years of erosion. 

The structures cost about $25 per foot of treated bank, or 20 to 50 percent of the cost of recent 

stone bank-stabilization projects in the region. 

Monitoring soil moisture throughout the world. Scientists from the National Aeronautics and 

Space Administration (NASA), the National Oceanic and Atmospheric Administration, the 

Natural Resources Conservation, and Alabama A&M University have joined ARS scientists 

from Beltsville, MD, in testing and designing satellites that will one day be able to monitor 

global soil moisture. The techniques use sensors that require an antenna that looks like an 

umbrella or a satellite dish. The technique functions like a mirror, constantly reflecting radiation 

emitted from Earth onto sensors that measure the strength of the radiation using microwave 

signals emitted from soil. The ARS scientists are testing these methods for a new satellite called 

Hydros that NASA plans to launch by the end of the decade. Once enhanced soil moisture 

predictions and measurements are part of daily weather forecasts it should help predict when 

rainstorms will occur; provide better assessments of drought stricken areas; provide needed 

information for assisting in alerting the public to potential floods; and help farmers determine 

when to plant, fertilize, and harvest crops with more precision and accuracy than has every been 

available before. 

Improved methods developed for estimating rainfall. ARS scientists in Boise, ID, working with 

the National Weather Service, developed new techniques to more accurately estimate rainfall 

using the National Weather Service (NWS) NAXRAD radar system. The ARS scientists found 

that the original methods NWS was utilizing under-estimated rainfall by 25 to 60% compared to 

NWS's measurements of precipitation on 6 highly instrumented experimental agricultural 

watersheds. NWS has reprogrammed the radar system in 2004 and has determined that the ARS 

derived technique has greatly improved the accuracy and precision of rainfall estimation. 

The U.S. Army gets help from ARS. The U.S. Army was looking for a way to determine realtime accurate estimates of surface soil moisture to help it plan where and when they can drive 

vehicles without getting stuck in the mud. The U.S. Army turned to ARS scientists in Tucson, 

AZ, to develop a method for rapidly and accurately estimating these conditions. The ARS 

scientists developed a new and simple remote sensing technique of image differencing in part by 

using data from the long-term highly instrumented Walnut Gulch watershed. This new 

procedure was found to be superior to the more complex and expensive model currently used by 

the U.S. Army because it can account for the high rocks content commonly found in desert soils. 

Water-treatment facility residues can help reduce water pollution. ARS scientists in Florence, 

SC, and University Park, PA, have found that residue from water-treatment processes, often 

discarded as waste and placed in landfills, may make a great soil amendment for preventing loss 

of phosphorus (P) in runoff from agricultural fields. ARS scientists have found an alum-based 

water-treatment residual that can increase the soil's capacity to bond phosphorus, a vital plant 

nutrient. The results should benefit states along the nation's mid- to-southern-Atlantic seaboard, 

where sandy soils generally take up and hold less P than finer-textured soils. In laboratory tests 

with sandy soil, the treatment increased P-binding potential four- to five-fold over that of 
untreated soil. If successful, this use for waste from water-treatment processing not only could 

get rid of the waste, but would also hold P on the land until a crop uses it. Economic benefits to 

the U.S. of reducing P in runoff are estimated to exceed at $200 million in addition to improving 

the quality of drinking water. 

Synchronizing fertilizer applications with crop needs. Technologies are needed to facilitate inseason application of nitrogen fertilizer to crops to reduce fertilizer input costs and the potential 

for nitrate losses. ARS scientists have devised management strategies for corn and cotton that 

apply nitrogen fertilizer during the growing season based on crop need. Aircraft and groundbased sensors were used to identify key wavebands that were indicative of crop nitrogen status 

and biomass production. Working with Resource21 and Holland Scientific, in conjunction with 

extensive ground-based crop and soil measurements, ARS scientists developed and tested 

requirements and specifications for passive and active crop canopy sensors for corn. A network 

of six ARS locations has evaluated the sensor on corn across the Midwest during the 2004 

growing season. ARS scientists also demonstrated that monitoring plant nitrogen status by 

spectral reflectance and chlorophyll meter measurements in cotton could be used to make realtime nitrogen management decisions reducing nitrogen application rates. A patent was issued 

for the apparatus and methodology of real-time, non-destructive determination of nitrogen need. 

A sensor developed through a CRADA with Holland Scientific and two related SBIR grants 

became commercially available in June 2004. Adoption of these practices can decrease on-farm 

costs, increase corn and cotton production, and decreases nitrate leaching. 

Removal of groundwater contaminants with buried bioreactors. Contaminated groundwater 

presents a health risk to both humans and animals and affordable treatment methods are needed 

to remove the contaminants from water. ARS scientists have demonstrated that buried in situ 

permeable bioreactors can be used to remove nitrate and organics from groundwater. 

Bioreactors can be composed of different organic materials such as wood chips or vegetable oil 

and are buried to intercept the contaminated ground water flow. The bioreactors stimulate 

natural microbial activity that denitrifies nitrite and nitrate to harmless dinitrogen gas and 

removes chlorate, perchlorate and heavy metals. Buried bioreactors can be used to remove 

nitrate from water below agricultural fields before it enters tile drains or to remove contaminants 

in ground water before entering wells or recharging surface waters. Farmers and industry to 

protect surface and ground water from animal wastes, fertilizer, can use bioreactors and chemical 

spills. 

Several commercial remediation firms are now using bioreactor technology. Sites contaminated 

with trichloroethylene (TCE) and spills at Travis Air Force Base, CA; Cape Canaveral Air 

Station, FL; Depot Hill, UT; Naval Support Activity Mid-South, TN and other military and 

civilian sites have been treated using vegetable oil injection. 

Long-term records critical for evaluating agriculture’s impact on hydrology and water quality. 

Given increased USDA expenditures to support the installation of conservation practices, there is 

a need to document the environmental improvements resulting from these investments. To do 

this, information is needed to understand the impacts of past management on current 

environmental conditions. Research conducted by ARS in Iowa is providing a better 

understanding of current hydrologic and water quality conditions in agricultural watersheds, and 

the time frame over which changes in management influence those conditions. Results showed 
the important role of high flows in delivering nitrate loadings to Midwest streams from 

subsurface drainage systems. Constructed wetlands within these watersheds would have limited 

effectiveness for removing nitrate during the high flows. Nitrate is also delivered to streams 

through base flow (ground water) contributions. Results show that nitrate in base flow can 

originate from nitrogen fertilizer applications made decades ago, even in small watersheds. 

Long-term records provide important perspectives for the evaluation of management systems, 

including conservation practices. Evaluation of conservation practices, installed today in 

individual fields, but evaluated at the outlet of watersheds must consider the full range of 

historical agricultural practices before accurate assessments of benefits can be accurately 

determined. These results remind us and encourage us that time and patience is required to 

improve water quality and we should not expect immediate recover when we install new 

conservation practices.