22 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Concerns about Elevated Nutrients in Water

The Clean Water Act of 1972 requires that States establish water-quality 

standards for water bodies, such as lakes and streams, “taking into consideration 

their use and value for public water supplies, propagation of fish and wildlife, 

recreational purposes, and agriculture, industrial, and other purposes, and also 

taking into consideration their use and value for navigation.” [Section 303(c)(2)(A)]. 

Although nitrogen and phosphorus are essential nutrients, elevated concentrations 

can lead to a variety of direct and indirect impairment of water bodies for many 

uses, including drinking water, recreation, and aquatic life. 

Drinking-Water Supplies and Human Health

The USEPA has set a standard of 10 mg/L as N of nitrate for drinking water to 

protect against methemoglobinemia, or “blue-baby syndrome,” a disorder in which 

the oxygen-carrying capacity of the blood is compromised. Intake of nitrate and 

nitrite in drinking water also has been implicated in other human health problems, 

including specific cancers and reproductive problems, although more research 

is needed to verify these associations (see Chapter 6 sidebar, Nitrate in Drinking 

Water: Potential Health Effects; Ward and others, 2005). Indirect effects of nutrient 

enrichment in surface waters on human health are numerous and complex. For 

example, algal blooms caused by nutrient enrichment may lead to algal toxins 

in water supplies (Lopez and others, 2008), an increase in the production of 

carcinogenic disinfection byproducts during chlorination of drinking water, and 

the potential for increased disease transmission due to an increase in mosquito 

populations (Townsend and others, 2003). Objectionable taste and odor are 

secondary issues related to nutrient-induced algal blooms that, while not a health 

hazard, are costly for drinking-water managers. 

Recreational Uses

Elevated nutrients can cause algal blooms and over-growth of other aquatic 

plants, which can cause aesthetic impairment, and interfere with recreational 

swimming and boating. In Nebraska, for example, the Department of Environmental 

Quality posts health alerts to warn residents when algal toxins reach levels unfit 

for recreational activities in specific lakes (Nebraska Department of Environmental 

Quality, 2009). 

Nutrients and Their 

Sources

Nutrients are essential for healthy 

plant and animal populations and provide 

a range of benefits, including increased 

food production for a growing global 

population. Too many nutrients, however, 

are not necessarily a good thing, and can 

have adverse effects on water quality, 

drinking‐water sources, recreation, and 

aquatic life (see sidebar, Concerns about 

Elevated Nutrients in Water). For example, 

excessive nitrate in drinking water can 

lead to “blue-baby syndrome,” in which 

oxygen levels in the blood become too 

low, sometimes with fatal results. Elevated 

concentrations of nitrogen and phosphorus 

in surface water can cause excessive growth 

of algae and other nuisance aquatic plants 

(a condition known as eutrophication). 

These plants can clog pipes and interfere 

with recreational activities such as fishing, 

swimming, and boating. Subsequent decay 

of algae can result in foul odors and a 

decrease in the amount of dissolved oxygen 

in water, also known as hypoxia. Hypoxic 

conditions, such as those found in the Gulf 

of Mexico, can harm fish and shellfish 

that are economically and ecologically 

important to the Nation. Societal concerns 

for the quality of our surface waters 

continue to increase, as many of the 

Nation’s streams and coastal waters do not 

meet water-quality goals. Data submitted 

by States in 2004, the most recent reporting 

date to the U.S. Environmental Protection 

Agency (USEPA) (2009), indicate that 

51 percent of the waters they surveyed are 

too contaminated for basic uses, such as 

fishing and swimming, because of their 

nutrient content.

In Nebraska, the Department of 

Environmental Quality posts health 

alerts to warn residents when algal 

toxins in lakes reach levels that make 

them unfit for recreational activities. 

Photograph courtesy of Tadd Barlow, 

University of Nebraska, Lincoln.
Chapter 2

Nutrient Primer 23

B.

Texas Louisiana

95° 90°

31°

30°

29°

28°

27°

26°

0 200 MILES

0 200 KILOMETERS

Bottom oxygen

values, in

milligrams per liter

0–2

2–4

4

Estuaries with low dissolved oxygen A.

Biological Condition of Freshwaters

Excessive nutrients and the resulting excessive 

plant biomass can have negative impacts on aquatic 

life. Increased plant biomass due to nutrient 

enrichment can cause a wide range of problems 

including a reduction in levels of dissolved oxygen 

(critical for aquatic life), decrease in quality of 

habitat, decrease in water clarity, enhancement of 

the growth of invasive species and toxic algae, and 

overall alteration of biological health (Lopez and 

others, 2008). Less often, ammonia concentrations 

reach levels toxic to fish, and national standards 

have been established for both acute and chronic 

exposure. In some settings and during different times 

of year, excessive nutrients can lead to “Harmful Algal 

Blooms,” or HABs, in which the population of algae 

grows to abnormal levels and either produces toxic 

compounds and (or) causes severe oxygen depletion 

associated with the die-off of the algal bloom 

(Bushaw-Newton and Sellner, 1999; Lopez and others, 

2008). HABs are most commonly found in eastern 

coastal waters and are due primarily to tiny marine 

organisms called dinoflagellates. Although HABs are 

less well documented in freshwater, most cases in 

northern States are associated with blue-green algae 

(Lopez and others, 2008); however, the golden algae 

Prymnesium parvum is documented as a producer of 

a potent toxin to fish in freshwaters in southern States 

(Lopez and others, 2008). 

Figure 2-1. Excess nutrients in runoff have resulted in hypoxia—low 

dissolved oxygen concentrations in water—in estuaries around the 

country (A), including the Gulf of Mexico (B). (A, modified from National 

Science and Technology Council Committee on Environmental and Natural 

Resources, 2003; and B, data from National Oceanic and Atmospheric 

Administration, 2004.)

Fish kill associated with a bloom of the golden algae, 

Prymnesium parvum, on Lake Whitney in Texas forms a 

silver band of dead fish along the shoreline. Photograph 

courtesy of Joan Glass, Texas Parks and Wildlife 

Department, from Lopez and others (2008).

Hypoxia in Coastal Waters and the Great Lakes

Most recently, HABs have been identified as a major cause of ecological 

disturbance in large water bodies. The decay of excessive algal biomass can 

deplete the dissolved oxygen in water, creating a condition called hypoxia 

(dissolved oxygen less than 2 mg/L). This can result in stress or death of 

near-bottom or bottom-dwelling organisms. Hypoxia in coastal regions that 

receive excess nutrients from rivers is a serious global problem, and hypoxic 

conditions plague critical waters in the United States including the Gulf of 

Mexico near the Mississippi River, the Chesapeake Bay, Puget Sound, and 

Lake Erie. Development of hypoxic conditions can have consequences for 

economic activities including fisheries and tourism (fig. 2-1).
24 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Nutrient Forms

Five measures of nitrogen- and phosphorus-containing 

nutrients are discussed in this report. All forms of nutrients 

discussed in this report are expressed as concentrations 

of either nitrogen or phosphorus. For example, a nitrate 

concentration expressed as 10 milligrams per liter (mg/L) 

refers to a nitrate concentration of 10 mg/L as nitrogen (as N).

• Total nitrogen includes nitrogen in all its forms—

nitrate, nitrite, ammonia, and organic nitrogen. Nitrite 

generally is unstable in surface water and contributes 

little to the total concentration of nitrogen in water. 

Organic nitrogen (mostly from plant material or organic 

contaminants) can exist in considerable proportions 

and contribute substantially to concentrations of total 

nitrogen in streams. 

• Nitrate, a compound of nitrogen and oxygen, is the 

primary form of nitrogen dissolved in streams and 

groundwater. In this report, nitrate refers to the sum 

of nitrate plus nitrite, because nitrite concentrations 

commonly were negligible. 

• Ammonia, a compound of nitrogen and hydrogen, 

is a dissolved form of nitrogen that is less common 

than nitrate. As measured by the USGS laboratory, 

total ammonia includes ammonium ion and un-ionized 

ammonia. Un-ionized ammonia typically is a minor 

component of ammonia at acidity levels (or pH levels) 

commonly observed in streams and groundwater. 

• Total phosphorus is usually bound to sediment, 

and generally includes dissolved phosphates and 

particulate organic phosphorus (mostly from 

plant material).

• Phosphates, compounds of phosphorus, oxygen, 

and hydrogen, typically constitute the majority of 

the dissolved phosphorus in natural water, and are 

referred to as orthophosphate. Orthophosphate can be 

readily assimilated by aquatic plants.

to a 2.5-fold increase in nitrogen- and phosphorus‐driven 

eutrophication (Tilman and others, 2001). Control of 

the delivery of these nutrients into the environment is 

complicated by cycling, in that nitrogen and phosphorus can 

be reintroduced into a system because of remobilization and 

biological activity long after nutrient inputs into the system 

have decreased. 

Nutrients Occur in Dissolved and 

Particulate Forms

Nutrients occur in several forms, including total 

nitrogen, nitrate, ammonia, total phosphorus and phosphate 

(see “Nutrient Forms”). Nitrogen forms available for plant 

uptake include dissolved inorganic nitrogen (ammonia, 

nitrate, and nitrite) and organic nitrogen. Nitrate is 

the primary form of nitrogen dissolved in streams and 

groundwater. Organic nitrogen, mostly from plant material 

or organic contaminants, can be dissolved or particulate 

(bound to sediment or in plant and animal tissue) and can 

contribute substantially to total nitrogen levels in streams. 

The most readily available form of phosphorus for 

plants is dissolved phosphate, which typically constitutes 

the majority of the dissolved phosphorus in natural water, 

and is generally reported as orthophosphate. In addition to 

dissolved phosphate, total phosphorus includes other forms, 

such as particulate organic phosphorus, which is mostly 

from plant material and usually bound to sediment.

Nutrients Occur Naturally but Most are 

Derived from Human Sources

Although nitrogen gas constitutes 78 percent of the 

Earth’s atmosphere, most plants and animals cannot utilize 

it directly, and therefore, they rely on processes that convert 

nitrogen gas into useable inorganic forms. For example, 

lightning and nitrogen “fixing” organisms, including 

legumes, bacteria, and algae, can convert nitrogen gas 

into biologically useable forms, such as ammonium and 

nitrate. Phosphorus also occurs naturally, in large part, from 

phosphate minerals in sediment and rocks. 

The natural global nitrogen cycle has been extensively 

altered through production and application of nitrogen 

fertilizers, cultivation of nitrogen-fixing crops, animal 

waste disposal, wastewater and industrial discharges, and 

combustion of fossil fuels (Galloway and others, 1995; 

Vitousek and others, 1997). These human alterations have 

approximately doubled the rate of nitrogen inputs into 

the terrestrial nitrogen cycle and have greatly increased 

the transfer of nitrogen from rivers to estuaries and other 

sensitive receiving waters. Human activities also have 

profoundly influenced the cycling of phosphorus through 

the environment, doubling the rate of phosphorus delivery 

from land to the oceans (Howarth and others, 2000).

The next 50 years will likely see rapid agricultural 

expansion in response to demand for food and a projected 

50-percent increase in global population, which could lead 
Chapter 2

Nutrient Primer 25

Human-Related Sources Include Point 

and Nonpoint Sources of Contamination

Human-related sources of nutrients can be 

classified as either point or nonpoint contamination. 

Point sources, such as those from municipal and 

industrial discharges and concentrated animal feeding 

operations, are regulated by laws that place limits 

on the types and amounts of contaminants that can 

be released to water. Legislation, starting in 1972 

with the Clean Water Act, has resulted in upgrades to 

wastewater-treatment plants and reductions in industrial 

sources of nutrients. Although violations still occur, 

legislation has had a positive influence on limiting the 

nutrients that enter water systems.

Nonpoint sources of nutrients include applications 

of commercial fertilizers on agricultural and residential 

lands, and nutrients from livestock and pet wastes 

and from septic systems. Atmospheric deposition 

also is a nonpoint source of nitrogen, which is 

derived either naturally from chemical reactions 

(such as through lightning) or from the combustion 

of fossil fuels, such as in coal-fired power plants, or 

volatilization of ammonia from fertilizer and manure 

(U.S. Environmental Protection Agency, 2002). Under 

some circumstances, nitrogen fixed by leguminous 

crops or stored in the soil can become a nonpoint 

source. Nutrients derived from nonpoint sources can be 

transported to streams in runoff from precipitation or 

irrigated fields, with inflowing groundwater, or through 

drainage ditches and subsurface tile-drain systems 

(hereinafter referred to as tile drains). 

Limiting nutrients from nonpoint sources is 

difficult because these sources are widespread and 

thus more difficult to identify and quantify than point 

sources. In fact, nonpoint-source contamination is 

the leading and most widespread cause of nutrient 

degradation of water; NAWQA studies estimate that 

more than 90 percent of nitrogen and phosphorus 

released to the environment originates from nonpoint 

sources (Puckett, 1995); the remaining percentages are 

from point sources.

Coal-fired power plants are sources of nitrogen in atmospheric 

deposition. Photograph by U.S. Geological Survey.
26 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Fertilizer is used extensively in corn and soybean growing areas of Iowa. 

Photograph by Lynn Betts, U.S. Department of Agriculture, Natural Resources 

Conservation Service.

17-0191_Fig_2-02_Nut_input.ai

0

2

4

6

8

10

12

14

1940 1950 1960 1970 1980 1990 2000 2010

Nutrient input, in millions of tons

Phosphorus in manure

(1982, 1987, 1992, 1997)

Phosphorus fertilizer

(1945–2006)

Atmospheric nitrogen

(1985–2001)

Nitrogen in manure

(1982, 1987, 1992, 1997)

Nitrogen fertilizer

(1945–2006)

EXPLANATION

Nutrient Sources Have Increased Over the 

Last Century but Have Remained Stable 

Since about 1980

The use of nitrogen and phosphorus fertilizers has 

increased over the last century, by 10-fold and 4-fold, 

respectively, between about 1950 and the early 1980s 

(fig. 2-2). The increase was due, in large part, to increases in 

areal application rates (the amount of fertilizer applied to each 

acre for some major crops) and an increase in the acreage 

of treated land. For example, the areal application rate of 

nitrogen fertilizer to corn grown in the Midwest increased 

from 49 to 129 pounds per acre from 1965 to 1980, after 

which it remained stable (Cassman and others, 2002). 

Since about 1980, applications of nitrogen and 

phosphorus fertilizers have leveled off and have since 

remained relatively stable (fig. 2-2). This is due in large part 

to increasing fertilizer costs, growing environmental concerns, 

and changing agricultural and waste management practices, 

which have reversed or slowed the pace of increasing use. 

Nitrogen and phosphorus from manure and nitrogen from 

the atmosphere also have remained relatively stable since the 

1980s (fig. 2-2).

Nationally, commercial fertilizer is the largest single 

nonpoint source of nutrients. More than 10 million tons of 

nitrogen and nearly 2 million tons of phosphorus are applied 

each year as commercial fertilizer (fig. 2-2). Most of the 

applications are for agricultural purposes, although a small 

portion, about 2 to 4 percent, of the total nitrogen fertilizer 

is used in nonagricultural settings such as city parks, golf 

courses, and residential lawns. 

About 6 million tons of nitrogen and nearly 2 million tons 

of phosphorus are excreted as manure each year. The mass of 

nitrogen in manure produced by livestock is about one-half 

as much as that applied in fertilizer and has varied little since 

data became available in 1982. The mass of phosphorus in 

manure is about the same as phosphorus applied in fertilizer, 

and also has varied little since 1982 (fig. 2-2). 

A significant proportion of the commercial fertilizer and 

manure that is applied to crops is taken up by the plants and 

removed from the fields, and hence does not contribute to 

environmental problems. Nitrogen uptake efficiencies have 

increased over the past two decades, and although uptake 

efficiencies as high as 80 percent in major cereal crops have 

been attained in controlled research experiments, uptake 

efficiencies on production farms usually range from 18 to 

49 percent (Cassman and others, 2002). 

Atmospheric deposition contributes about one-half as 

much nitrogen as manure does, and less than one-quarter as 

much nitrogen as does fertilizer application. Specifically, 

about 2.5 million tons of nitrogen are deposited in the United 

States each year from the atmosphere (fig. 2-2). Phosphorus 

generally does not enter the environment with 

atmospheric deposition. 

Figure 2-2. The use of nitrogen and phosphorus fertilizers has 

increased 10-fold and 4-fold, respectively, between about 1950 

and the early 1980s. Since about 1980, however, applications of 

nitrogen and phosphorus fertilizers have leveled off and have 

remained relatively stable. Nitrogen and phosphorus from manure 

and nitrogen from the atmosphere also have remained relatively 

stable since the 1980s. (Modified from Ruddy and others, 2006.)
Chapter 2

Nutrient Primer 27

Figure 2-3. Different sources of nitrogen and phosphorus predominate in streams that represent different land-use 

categories. (See table 3-1 for definition of land-use categories.)

Figure 2-4. Both the areal rate of fertilizer application (A) and the total use 

(B) vary widely among major crops (U.S. Department of Agriculture, 2006).

0 20 40 60 80

Nutrient input, in percent

Mixed

0 20 40 60 80

Nutrient input, in percent

Undeveloped

0 20 40 60 80

Nutrient input, in percent

Urban

0 20 40 60 80

Atmospheric

Nonfarm

fertilizer

Manure

Farm

fertilizer

Phosphorus

Nitrogen

Agricultural

Nutrient input, in percent

Data on atmospheric phosphorus inputs not available.

Phosphorus

Nitrogen

0 75 150

Soybeans

Cotton

Wheat

Corn

Average nutrient application rate,

by selected crop, 1997,

in pounds per fertilized acre

A. B.

0 2 4 6

Soybeans

Cotton

Wheat

Corn

Estimated nutrient use,

by selected crop, 1997,

in millions of tons

Sources of Nutrients by Land Use and Crop Type

The NAWQA approach to categorizing stream basins results in different sources of nitrogen and phosphorus predominating 

in streams that represent different land-use categories. Commercial fertilizers constitute more than 60 percent of nitrogen and 

phosphorus inputs to agricultural basins, and more than 50 percent to urban basins (fig. 2-3). Manure also can be a significant 

source of nutrients in agricultural watersheds, accounting for about 25 percent and nearly 40 percent, respectively, of nitrogen 

and phosphorus inputs. Animal manure on pasture and rangelands, and atmospheric deposition, are the largest contributors of 

nutrients in undeveloped lands.

In general, the use of commercial 

fertilizers on agricultural land varies, 

depending on the type of crop, with 

the highest areal rates of application 

on corn (about 130 pounds of nitrogen 

per acre; fig. 2-4A). Corn also received 

the largest proportion of nitrogen from 

commercial fertilizer, representing 

about 40 percent of the total use in 1997 

(fig. 2-4B). In contrast, the areal rate of 

nitrogen fertilizer application on soybean 

plants is relatively low (about 30 pounds 

per acre; fig. 2-4A) because bacteria in 

the roots of soybean plants are capable 

of extracting, or “fixing,” nitrogen gas 

from the atmosphere. As a consequence, 

less than 2 percent of the nitrogen 

from commercial fertilizer was used on 

soybean cultivation in 1997 (fig. 2-4B). 
28 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

From about 1940 to 1970, laundry 

detergent was a major source of phosphorus 

to the environment. Contributions decreased 

to almost negligible amounts, however, after 

the enactment of State bans on the use of 

phosphate detergent beginning in the 1970s 

and the voluntary cessation of phosphate use 

by detergent manufacturers. As a result, the use 

of phosphorus in detergents decreased from a 

peak of 220,000 metric tons in 1967 to less than 

10,000 metric tons in 1995 (Litke, 1999).

Sources of ammonia also have decreased 

since the early 1970s when legislation was 

enacted to improve the treatment of wastewater. 

The decreased ammonia concentrations achieved 

through treatment nitrification (or the oxidation 

of ammonia to nitrate) of wastewater prior to 

discharge also has increased levels of dissolved 

oxygen in streams, which can help to improve 

the health of fish communities. However, 

because ammonia is converted to nitrate during 

nitrification, nitrate has increased in some 

streams downstream from wastewater-treatment 

plants, such as in the Trinity River, Texas (see 

Chapter 8 sidebar, Past Changes Resulting from 

Nutrient Control Measures).

Sources of Nutrients Vary 

Geographically and by Land Use

The relative contributions of the different 

nonpoint nutrient sources vary in different 

geographic regions of the country (fig. 2-5) and 

can be explained, in large part, by the distribution 

of agricultural, urban, and undeveloped land 

use (see sidebar, Sources of Nutrients by 

Land Use and Crop Type). The highest rates 

of farm fertilizer nitrogen application are in 

the upper Midwest, where an application rate 

of 40,000 pounds per square mile (lb/mi2) is 

exceeded over an extensive area from Indiana to 

Nebraska. Farm fertilizer nitrogen application 

rates are also high in parts of the irrigated West, 

such as the Snake River Plain in southern Idaho, 

California’s San Joaquin Valley, parts of Florida, 

and parts of the east coast. 

Some parts of the Southeast and Southern 

Plains and the extensive western rangelands 

receive high loads of nitrogen (locally exceeding 

40,000 lb/mi2) in the form of manure, but 

such areas of high manure applications are not 

as extensive as those of high applications of 

commercial fertilizers. Manure from animals that 

are restricted to confined feeding operations, such 

as at dairies or feedlots, is usually stored onsite 

for later use on adjacent agricultural land; manure 

from free-ranging livestock is not recovered, 

but rather is distributed across the grasslands, 

shrublands, and forests used for grazing. 

Nitrogen applications of nonfarm fertilizer, 

such as that used on lawns in residential areas, 

generally are restricted to population centers, and 

rarely exceed 10,000 lb/mi2 outside of densely 

populated areas (fig. 2-5). 

Atmospheric sources of nitrogen are highest 

in the eastern part of the country, where the 

deposition rates are highest (fig. 2-5). In general, 

the rate of atmospheric deposition of nitrogen 

increases progressively from the west to east. The 

highest deposition rates of nitrogen occur in a 

broad band from the upper Midwest through 

the Northeast. 
Chapter 2

Nutrient Primer 29

Figure 2-5. The highest rates of commercial fertilizer applications of nitrogen are in agricultural areas of the upper Midwest, and 

parts of the Great Plains, the Northwest, California, and the southeast Atlantic Coastal Plain. Commercial fertilizers also are a leading 

source of nutrients in urban areas around the Nation. Manure sources dominate in parts of the South and Southeast and in extensive 

western rangelands. Atmospheric sources are highest in the eastern part of the country, where the deposition rates are highest, and 

increase from west to east.

17-0191_Fig_2-05_NInput_Maps_newcat_addlmap.ai

Nitrogen from sewage

Nitrogen from nonfarm fertilizer Nitrogen from atmospheric deposition

Nitrogen from farm fertilizer Nitrogen from livestock manure

Estimated 1997 nitrogen input rate from farm and nonfarm fertilizer, 

manure, atmospheric deposition, and sewage, in pounds 

per square mile

0–≤1,000

1,000–≤2,000

2,000–≤3,000

3,000–≤4,000

4,000–≤5,000

5,000–≤6,000

6,000–≤8,000

8,000–≤10,000

10,000–≤20,000

20,000–≤30,000

30,000–≤40,000

40,000

No nutrient input

EXPLANATION
30 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Connecticut River, Connecticut

Susquehanna River, Pennsylvania White River, Indiana

Palouse River, Washington

San Joaquin River, California 

South Platte River, Colorado 

White River, Arkansas

Proportions of 

nitrogen sources for

selected watersheds

Atmosphere

Fertilizer Manure

Sewage

Fertilizer

Manure

Atmosphere

Sewage

EXPLANATION

Dominant source 

of nitrogen, by county

Different Sources of Nitrogen Predominate 

in Different Regions of the Country

Fertilizer is the predominant source of nitrogen in 

most agricultural areas (fig. 2-6), including in the Midwest 

and Great Plains (White River Basin, Indiana), the 

irrigated West (Palouse River Basin, Washington, and the 

San Joaquin River Basin, California), and in parts of the 

Southeast. Nutrients from manure, however, can dominate 

those from commercial fertilizers in some agricultural 

watersheds with large populations of confined livestock, 

such as in parts of the East, South, and Southeast (see areas 

exceeding 40,000 lb/mi2, fig. 2-5), including in the White 

River Basin in Arkansas, the Susquehanna River Basin in 

Pennsylvania, and in the extensive western 

rangelands (fig. 2-6).

Some urban watersheds receive significant nutrient inputs 

from wastewater-treatment plants, such as in the South Platte 

River Basin, Colorado (fig. 2-6). Occasionally, streams are 

dominated by wastewater effluent from treatment plants; this 

circumstance is more common in urban areas of the semiarid 

West, including parts of Arizona, Nevada, and southern 

California, where wastewater-treatment plant effluent may 

be the predominant source of water in a stream during

 dry seasons.

Atmospheric deposition is the largest nonpoint source 

of nitrogen in undeveloped watersheds in the eastern part of 

the country where the deposition rates are highest, such as in 

the Connecticut River Basin, Connecticut (fig. 2-6), and in 

areas near the Great Lakes and the arid and mountainous West 

where human development is very sparse.

Figure 2-6. Commercial fertilizers are the dominant source of nitrogen in the White River Basin in Indiana, 

which is typical of their intensive use in the upper Midwestern part of the Nation, and in parts of the Northwest 

and West, such as in the Palouse River Basin in Washington and the San Joaquin River Basin in California. 

Commercial nitrogen fertilizers also are the major source of nitrogen in urban basins, and some urban watersheds 

also have significant nutrient contributions from wastewater-treatment plants, such as in the South Platte River 

Basin, Colorado. Nutrients from manure can even dominate those from commercial fertilizers in some agricultural 

watersheds with large populations of confined livestock, such as in the White River Basin in Arkansas and in the 

Susquehanna River Basin, Pennsylvania, as well as in the extensive western rangelands. Atmospheric contributions 

of nitrogen are important in the eastern parts of the country, such as in the Connecticut River Basin.
Chapter 2

Nutrient Primer 31

Streams are particularly

vulnerable to nutrient

contamination because runoff

from agricultural and urban

areas flows directly into streams

along with both dissolved and

particle-associated nutrients.

Nonpoint sources are diffuse 

and widely dispersed, such as 

agricultural runoff and 

atmospheric deposition.

Nitrogen is transported to the 

atmosphere by burning of fossil 

fuels and may also volatilize 

from fertilizer and manure.

Nutrients are transported to 

groundwater mostly by recharge 

resulting from rainfall or irrigation 

within agricultural and urban 

areas. Other locally important 

sources include transport down 

leaky well casings and contaminated streams that lose water to 

the groundwater system.

Point-source contamination can

be traced to specific points of

discharge from wastewatertreatment plants and factories

or from combined sewers.

REGIONAL TRANSPORT

The atmosphere is a primary source of

nitrogen, which returns to earth with precipitation 

and dry deposition. In the natural nitrogen cycle, 

nitrogen gas in the atmosphere is converted to 

biologically-available forms by bacteria in soils or 

associated with plants.

Groundwater is an important source of 

nutrients to some streams during 

low-flow periods, when groundwater 

constitutes a major portion of streamflow.

DRY

DEPOSITION

GROUNDWATER RECHARGE

DISCHARGE

TO STREAMS

RUNOFF

RECHARGE

FROM

STREAMS

PRECIPITATION

ENTRY

THROUGH

WELLS

WASTEWATER

EVAPORATION

SPRAY DRIFT

WIND EROSION

RUNOFF

RECHARGE

Figure 2-7. Nutrients from nonpoint and point sources are cycled throughout the hydrologic system, but may be affected by different 

chemical, physical, and biological processes in different parts of the system. (Modified from Majewski and Capel, 1995.)

Nutrient Transport to Streams and 

Groundwater

Nutrients released into the environment as diffuse 

nonpoint sources or as point sources enter streams along with 

runoff from precipitation, irrigation, or through drainage 

ditches and tile drains; are transported to groundwater by 

infiltrating rainfall or irrigation; and are transported to the 

atmosphere by volatilization either directly from a source or 

from a contaminated surface-water body (fig. 2-7). Within 

each of the hydrologic compartments, nutrient concentrations 

are affected by physical features, such as soils and slope of 

the land, as well as by biological and geochemical processes 

that can change the chemical form of the nutrient and (or) 

transfer it from the water to a solid phase or to the atmosphere. 

The chemical, physical, and biological processes that 

influence nutrient transport vary in intensity among different 

environmental settings. 
32 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Agricultural Best Management Practices

Agricultural best management practices (BMPs) are designed to minimize the environmental impacts of 

agriculture while sustaining crop productivity. BMPs reduce nutrient losses to streams through management 

of nutrient inputs on the land surface and through curtailment of erosion and runoff of nutrients from the 

land surface to streams. Three common BMPs are conservation tillage, nutrient management plans, and 

conservation buffers (U.S. Environmental Protection Agency, 2008). 

• Conservation tillage—Conventional tillage exposes the soil surface by plowing crop residues into 

the soil. In contrast, conservation tillage limits tilling while retaining crop residue on the soil surface, 

thereby increasing infiltration and reducing erosion and runoff to streams.

• Nutrient management plans—Comprehensive nutrient management plans help guide decisions on 

the placement, rate, timing, form, and method of nutrient application to avoid inputs in excess of crop 

requirements and to minimize loss to streams, groundwater, or the atmosphere. Nutrient management 

plans can incorporate a variety of agronomic tests to balance the amount of nutrients currently 

available in the soil against the amount required for crop production, and to identify the ideal timing 

for crop growth and irrigation to minimize runoff and leaching.

• Conservation buffers—Conservation buffers are areas of permanent vegetation often planted 

adjacent to streams, lakes, ponds, and wetlands or along the edges of agricultural fields to help 

reduce runoff or leaching of nutrients by filtering out nutrients and sediments, enhancing infiltration, 

and increasing plant uptake. The vegetation in buffers also can provide wind breaks, wildlife habitat, 

cooler water temperatures, stream-bank stabilization, and improved aesthetics.

BMPs often are included as part of cooperative conservation plans developed through the U.S. 

Department of Agriculture’s (USDA) Farm Service Agency and Natural Resources Conservation Service, 

other Federal, State, and local agencies, private companies, and individual landowners. Four of the largest 

national USDA conservation programs are the Conservation Reserve Program (CRP), the Conservation 

Reserve Enhancement Program (CREP), the Wetlands Reserve Program (WRP), and the Grassland Reserve 

Program (GRP). These programs are all voluntary. Farmers, ranchers, and other producers enrolled in the 

CRP plant long-term vegetative covers, such as introduced or native grasses or hardwood trees, to improve 

water quality, control soil erosion, and enhance wildlife habitat. As of 2008, 34.72 million acres were enrolled 

in the CRP (U.S. Department of Agriculture, 2008). The CREP, which is part of the CRP, helps producers 

protect environmentally sensitive land, decrease erosion and runoff, restore wildlife habitat, and safeguard 

groundwater and surface water through BMPs such as conservation buffers. As of 2008, 1.13 million 

acres were enrolled in the CREP (U.S. Department of Agriculture, 2008). The WRP provides landowners 

financial incentives and technical assistance to restore wetland functions while maximizing wildlife habitat 

benefits. Wetlands reduce downstream flooding, protect drinking water, filter runoff, and provide vital 

habitat for many wildlife species. As of 2008, 2.0 million acres were enrolled in the WRP (U.S. Department 

of Agriculture, 2008). The GRP helps landowners restore and enhance grasslands on their property and 

protects vulnerable grasslands from conversion to crop land, urban land, or other uses. The GRP has 

enrollments in all 50 States and Puerto Rico (U.S. Department of Agriculture, 2008).

Measuring the cumulative effect of BMPs on water quality in streams across the Nation is a challenging 

task. In the large watersheds studied by the NAWQA Program, which range from less than 8 square 

miles to more than 80,000 square miles, BMPs are one of many influences on water quality in streams. 

Distinguishing the effects of BMPs from the effects of often interrelated changes in land use, source 

inputs, climate, or other factors can be a difficult task—a task that is further complicated by the lack of 

comprehensive national-scale data on when and where various BMPs are implemented across the Nation. 

More comprehensive and detailed data on BMPs could help improve our understanding of the factors 

affecting nutrient conditions in the Nation’s streams and groundwater. Our understanding of the effects of 

BMPs on agricultural landscapes will be advanced by a multi-scale assessment of the environmental effects 

of conservation practices and programs being conducted by the USDA’s Conservation Effects Assessment 

Program (U.S. Department of Agriculture, 2010).
Chapter 2

Nutrient Primer 33

Assessment of the occurrence and transport 

of nutrients in streams and groundwater, 

therefore, requires recognition of complicated 

interconnections among surface water and 

groundwater systems, atmospheric contributions, 

and the natural and human factors that can 

affect transport. Key natural factors, including 

soil type, geology, and slope of the land, can 

govern the amount and timing of transport of 

nutrients to streams and groundwater. Human 

factors and actions that can affect transport 

include irrigation, groundwater pumping, the 

presence of impervious surfaces, artificial 

subsurface drainage, and best management 

practices (see sidebar, Agricultural Best 

Management Practices). The result can be 

varying concentrations of nutrients in streams 

and groundwater, even in watersheds that may 

have similar land-use settings and rates of 

fertilizer use. 

Nutrient transport in water depends on the 

chemical makeup of the nutrients themselves, 

which can affect mobility and persistence. 

Some compounds, such as nitrate, readily 

dissolve and move with water in both streams 

and groundwater. Most forms of phosphorus, 

however, attach to soil particles rather than 

dissolve; these compounds are transported 

to streams with eroded soil, particularly 

during times of high runoff from precipitation 

or irrigation. Groundwater typically is not 

vulnerable to contamination by nutrients, such as 

phosphorus, that attach to soils. 

Nutrient transport in water also depends on 

geochemical conditions of the water, which can 

affect the persistence of a nutrient. For example, 

as long as dissolved oxygen is present in 

groundwater (referred to as oxic conditions) and 

organic carbon content is low, nitrate generally 

is stable and hence persistent in groundwater, 

sometimes for decades (see sidebar, Redox 

Conditions in Aquifers Affect the Stability of 

Nitrate in Groundwater). Groundwater inflow 

to streams, therefore, can be a large source of 

nitrate in some areas (Bachman and others, 

1998; Sprague and others, 2006). If the dissolved 

oxygen in groundwater is depleted, nitrate 

becomes unstable and is converted to nontoxic 

nitrogen gas, a process referred to 

as “denitrification.”

Conservation tillage allows for double-cropping 

of soybeans in the residue left by winter wheat, 

yielding two crops during a single growing season 

and protecting the land from erosion. Photograph 

by Joseph Larson, U.S. Department of Agriculture, 

Natural Resources Conservation Service.

Multiple rows of trees and shrubs, as well 

as a native grass strip, combine in a riparian 

conservation buffer to protect Bear Creek in Story 

County, Iowa. The buffer is a nationally designated 

demonstration area for riparian buffers. Photograph 

by Lynn Betts, U.S. Department of Agriculture,

Natural Resources Conservation Service.
34 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Streams

The transport of nutrients to streams is driven by 

precipitation or irrigation. In large part, it is driven by the 

timing of the precipitation and associated runoff and drainage 

relative to fertilizer and manure applications, and controlled 

by a multitude of natural and human factors that affect runoff 

and groundwater discharge to streams. Specifically, high 

rainfall, snowmelt, and (or) excessive irrigation, especially 

following recent fertilizer applications, can accelerate 

transport of nutrients to streams. Streams with steep slopes 

and sparse streamside vegetation to slow runoff and sediment 

movement generally are vulnerable to nutrients entering 

their channels. Clayey and compacted soils underlain by 

poorly drained sediment and (or) nonporous bedrock can 

create relatively impermeable surfaces for quick runoff, as 

can extensive urban pavement. Flat areas with tile drains and 

ditches also can provide quick pathways for runoff to streams. 

In contrast, some best management practices help to reduce 

transport of nutrients, particularly those nutrients that bind 

to soil and sediment, such as phosphorus. Examples of such 

practices include (1) the use of polyacrylamide, a chemical 

added to irrigation water to reduce erosion and enhance water 

infiltration, and (2) conversion from rill irrigation to sprinkler 

and drip irrigation systems, which use less water and thereby 

reduce erosion and surface runoff. 

The biology and physical habitat of a stream also can 

affect the transport and occurrence of nutrients in streams. 

Once nitrogen enters a stream, it cycles in and out of the 

water as a result of the activities of plants and animals. 

Production of plant biomass cycles nutrients from the water, 

while decay of plants and animals cycles nutrients back into 

the water. As nutrients cycle between the water and biota, 

they can be eventually lost to the stream either by exchange 

with the atmosphere (in the case of nitrogen) or by transport 

downstream. Nitrogen and phosphorus can both limit 

biological production, with streams in the eastern United 

States more likely to be phosphorus-limited and streams in the 

Western United States more likely to be nitrogen-limited. 

Three physical habitat factors—light, water temperature, 

and streamflow—affect the development and growth of algae 

and aquatic plants, which can thereby affect nutrient uptake 

and hence the subsequent transport of nutrients in a stream. 

Overhanging riparian vegetation can block light from reaching 

the water surface, and suspended sediments can increase 

turbidity and prevent light from penetrating the water. Growth 

of algae and aquatic plants is limited by low-light conditions, 

regardless of nutrient concentrations. Water temperature can 

regulate the rate at which cells can function and grow, with 

warmer water temperatures stimulating more rapid plant 

growth. Streamflow can limit the growth of algae and other 

aquatic plants by limiting nutrient and habitat availability 

during periods of low flow, or by scouring the bottom of the 

stream and reducing the abundance of attached vegetation 

during periods of high flow, such as after a heavy rainfall.

Groundwater

As with streams, transport of nutrients to groundwater 

is driven by precipitation or irrigation, which provide sources 

of water for recharge. Groundwater transport of nutrients is 

different from that in streams because only dissolved forms 

of nutrients can move substantial distances in groundwater. 

Nitrate readily dissolves and moves with water, and is 

therefore often the dominant nutrient species. Particle bound 

constituents, like phosphorus, are largely retained by the soil 

and aquifer materials. In addition, transport of nutrients to 

and within groundwater systems is much less predictable than 

transport in streams because flow is considerably slower and 

more complex than the flow of stream water. 

Natural features that accelerate nutrient transport to 

groundwater generally contrast with those discussed above for 

streams. Nitrate is readily transported to shallow groundwater 

in well-drained areas with rapid infiltration and highly 

permeable subsurface materials. Well-drained and permeable 

soils that are underlain by sand and gravel or carbonate rock 

(also referred to as “karst”) can enable rapid downward 

movement of water. Crop-management practices, which 

commonly are designed to reduce or slow the movement of 

sediment and nutrients to streams, also can increase infiltration 

of water and nutrients into the ground. Pumping groundwater 

can accelerate the flow of water and transport contaminants 

toward the pumped wells. 

Physical characteristics of streams, such as the amount of shading, influence 

nutrient transport. Photograph by U.S. Geological Survey.
Chapter 2

Nutrient Primer 35

390

396

402

408

414

420

426

432

Elevation, in meters

Water table

Otter Tail River

EXPLANATION Datum is sea level

Vertical scale greatly exaggerated

0 500 1,000 METERS Age of groundwater, in years

0–10

10–30

30–40

40

Redox Process

Oxygen reduction

Nitrate reduction

Iron reduction

Carbon dioxide reduction

Sand and gravel

surficial aquifer

Well cluster Land surface

Boundary (dashed where inferred)

Glacial

till

Well screen 

location

Otter Tail River, Minnesota

Redox Conditions in Aquifers Affect the Stability of Nitrate in Groundwater

Under the right conditions, nitrate may be removed from groundwater before it reaches the intake 

screen of a drinking-water well by a biogeochemical process called denitrification. In aquifers, bacteria 

are constantly breaking down natural organic carbon compounds to acquire the energy they need to 

live in much the same way that humans break down the organic carbon compounds in the food we 

eat. Because carbon is oxidized (by losing an electron) and other reactants are reduced (by gaining 

an electron), these are known as oxidation–reduction, or “redox” reactions. Less often, an inorganic 

constituent, such as the reduced form of iron in the minerals pyrite and glauconite, is oxidized. In 

the first reaction in the sequence, bacteria utilize the oxygen dissolved in groundwater to oxidize the 

available organic carbon. As long as dissolved oxygen is present in groundwater, nitrate is generally 

stable and hence persistent. Groundwater containing dissolved oxygen concentrations greater than 0.5 

mg/L is referred to as “oxic.” As oxygen is consumed, groundwater becomes reduced (concentrations 

of dissolved oxygen less than 0.5 mg/L). If dissolved oxygen in groundwater becomes depleted, the 

bacteria will use nitrate to oxidize the organic carbon in a redox reaction called denitrification. Through 

denitrification, nitrate (NO3

-) is converted to nitrogen gas (N2

), which is nontoxic. After nitrate is mostly 

gone, then bacteria can use organic carbon for other redox reactions such as manganese reduction, iron 

reduction, sulfate reduction, and reduction of carbon dioxide to methane. As a result of these reactions, 

nitrate may be removed from the groundwater, only to be replaced by manganese, iron, sulfide, or 

methane (considered markers of reduced waters). Often these various processes occur in succession as 

water moves down and through an aquifer, creating a layered or stratified sequence of water chemistry 

(fig. 2-8).

Figure 2-8. Biogeochemical processes can occur in succession as water moves down and through an aquifer, 

creating a layered or stratified sequence of water chemistry. In the aquifer adjacent to the Otter Tail River, 

Minnesota, nitrate is removed from the groundwater by denitrification in a zone near the water table. (Modified 

from Puckett and Cowdery, 2002.) 
36 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Natural processes can significantly reduce nutrient 

concentrations in groundwater through chemical and 

biological transformations under the right geochemical, 

or “redox,” conditions (see sidebar, Redox Conditions in 

Aquifers Affect the Stability of Nitrate in Groundwater). 

Through denitrification, bacteria can convert nitrate to 

innocuous, gaseous forms of nitrogen when groundwater 

passes through organic-rich sediment that is low in 

dissolved oxygen. 

Deep aquifers usually contain water with lower 

concentrations of nutrients than shallow aquifers because (1) it 

takes a long time—decades or more, in most cases—for water 

to move from the land surface to deep aquifers (resulting in 

long residence times for groundwater and any solutes, like 

nitrate, it may contain); (2) long travel distances increase 

the likelihood that nutrients will transform, such as through 

denitrification, or attach to aquifer materials; (3) protective 

low-permeability deposits (which inhibit flow and transport) 

may be present between the land surface and deep aquifers; 

and (4) mixing of water from complex flow paths over long 

distances and time periods tends to result in a mixture of landuse influences on the chemical character of deep groundwater, 

including contributions of nutrients from areas of undeveloped 

lands where concentrations are generally lower than those 

from developed lands.

It is important to note that groundwater at all depths is 

part of an integrated and interconnected hydrologic system and 

is subject to contamination as water moves downward from 

the land surface. Future contamination in deep major aquifers 

could pose serious concerns because these aquifers commonly 

are sources of private household and public water supplies, 

and restoration of the purity of this relatively inaccessible and 

slow-moving water would be costly and difficult.

Transport of Nutrients Varies Seasonally and 

with Hydrologic Events

Transport of nutrients to streams and groundwater 

varies seasonally, in large part following seasonal patterns in 

human activities. For example, in Granger Drain, Washington, 

concentrations of nitrate are highest during the non-irrigation 

season when groundwater is the primary source of water to the 

stream (fig. 2-9). Concentrations of total phosphorus, however, 

are highest during the irrigation season, when surface runoff 

delivers phosphorus-rich sediment to the drain. 

The transport of nutrients to streams also can vary 

in response to changes in precipitation and runoff and 

streamflow (see sidebar, Effects of Precipitation and 

Climate on Streamflow and Temporal Variability of Nutrient 

Concentrations). Increases in precipitation and streamflow 

in basins in which point-source discharges or nitrate-rich 

groundwater inflows predominate commonly are accompanied 

by decreases in nutrient concentrations as a result of greater 

instream dilution by the relatively clean runoff. The same 

increase in precipitation and streamflow in basins in which 

nonpoint sources predominate, however, can increase nutrient 

concentrations as a result of increased transport by surface 

runoff. For example, in the Hockanum River, which drains 

an urban watershed in Connecticut, greater dilution of the 

relatively constant nutrient input from point sources led to 

lower total phosphorus concentrations at higher streamflows 

(fig. 2‐10). The opposite pattern occurred in Sugar Creek, 

which drains an agricultural watershed in Indiana—increased 

nutrient transport in surface runoff from extensive corn 

and soybean fields upstream led to higher total phosphorus 

concentrations at higher streamflows.

The transport of nutrients to streams also can vary 

seasonally in response to rates at which nutrients are taken out 

of the water during growth by aquatic organisms (“uptake”). 

For example, total nitrogen concentrations were lowest in late 

summer in some agricultural streams due to biological uptake 

and relatively low rates of fertilizer applications. 
Chapter 2

Nutrient Primer 37

May June July Aug Sept Oct Nov Dec Jan

Total phosphorus concentration,

in milligrams per liter

0

0.2

0.4

0.6

0.8

1.0

1.2

Nitrate concentration,

in milligrams per liter as N

0

1

2

3

4

5

6

7

Irrigation season Non-irrigation season

1999 2000

Granger Drain at Granger, Washington

Total phosphorus concentration

Nitrate concentration

EXPLANATION

Streamflow, in cubic feet per second

Sugar Creek at New Palestine, Indiana

0 500 1,000 1,500 2,000

0.0

0.1

0.2

0.3

0.4

0.5

Hockanum River near East Hartford, Connecticut

Total phosphorus concentration,

in milligrams per liter

0 100 200 300 400 500 600 700

0.0

0.2

0.4

0.6

0.8

1.0

Part of the flow of the Yakima River is diverted to provide irrigation 

water for crops in Central Washington. Photograph by Henry Ngam, U.S. 

Geological Survey.

Figure 2-9. Concentrations of nitrate and total phosphorus 

in Granger Drain, Washington, vary in response to their major 

transport pathways. Nitrate concentrations are highest during 

the non-irrigation season, when groundwater is the primary 

source of water to the stream, whereas total phosphorus 

concentrations are highest during the irrigation season, when 

surface runoff transports phosphorus-rich sediment to the 

stream (Fuhrer and others, 2004). 

Figure 2-10. Total phosphorus concentrations in the Hockanum River, Connecticut, an urban site with 

numerous upstream point sources, decreased as streamflow increased because of greater instream 

dilution. In contrast, total phosphorus concentrations in Sugar Creek, Indiana, increased as streamflow 

increased as a result of greater surface runoff from extensive fields of corn and soybeans.
38 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Figure 2-11. Areas of the conterminous United States where long-term droughts 

(several years to decades) are positively correlated (red) or negatively correlated (blue) 

with changes in ocean temperature in the North Pacific (A) and the North Atlantic (B). 

(Modified from McCabe and others, 2004.)

A.

B.

Positive values are shaded red, and negative values are shaded 

blue. Darker shades indicate stronger correlation (>0.4 or <-0.4).

Effects of Precipitation and Climate on Streamflow and 

Temporal Variabilitiy of Nutrient Concentrations

Michael Dettinger, U.S. Geological Survey

Daily, seasonal, and long-term changes in climate can affect streamflow, which in turn affects nutrient 

variability in streams. Specifically, daily variability in surface temperature, light availability, and precipitation 

can contribute to short-term (minutes to days) changes in local hydrologic processes such as runoff, 

snowmelt, and evapotranspiration, that in turn affect streamflow. Seasonal changes (weeks to months) in 

large-scale weather patterns can bring seasonal dry or wet periods and the start and end of growing seasons. 

Longer changes (years) are tied to “El Nino” events in the tropical Pacific, which yield a recurring pattern 

of winter precipitation that favors a wetter-than-normal Southwest and Florida and a drier-than-normal 

Northwest. The opposite of an El Nino in the tropical Pacific is a “La Nina,” which reliably yields wetterthan-normal winters in the Northwest and drier-than-normal winters in the Southwest. Changes that last for 

decades at a time, such as prolonged droughts, are related to climatic fluctuations over the North Pacific and 

North Atlantic (fig. 2-11).
Chapter 2

Nutrient Primer 39

Onset of spring snowmelt

>20 days earlier

15–20

10–15

5–10

between 5 days earlier and 5 days later

5–10 days later

10–15

15–20

>20

Large circles indicate sites with trends that differ significantly from 

zero at 90-percent confidence level; small circles are not confidently identified.

140° 130° 120° 50°

45°

40°

35°

110°

Additional multi-decadal streamflow variability may be related to long-term climate change in 

response to increasing greenhouse-gas concentrations in the global atmosphere, or to naturally 

occurring variability in winter and spring temperatures and in the form and timing of precipitation. 

Warming has occurred across the West, upper Midwest, and Northeastern United States, while the 

Southeast has actually cooled overall. Warmer winters and springs in the Western United States 

have contributed to widespread hydrologic changes, including trends towards more precipitation as 

rain rather than as snow, less snowpack overall, earlier greening of vegetation, and earlier snowmelt 

(fig. 2-12).

Figure 2-12. Spring snowmelt onset—the date on which snowmelt runoff adds a large 

initial surge to rivers—occurs a week to almost three weeks earlier now than in the middle 

of the 20th century in the West (Dettinger, 2005). Changes in the timing of streamflow have 

implications for agricultural water management and hence nutrient transport. 

Nutrient concentrations respond to these short-term and longer-term temporal changes in 

streamflow. Specifically, nutrient concentrations can change throughout the year and over a 24-hour 

period in response to changes in light availability, temperature, and in turn, biological productivity 

(Kent and others, 2005; Peterson and others, 2005). Concentrations in some areas are highest during 

spring and summer wet periods following fertilizer application. Concentrations in other areas are 

highest during winter low-flow periods because of groundwater inflow and reduced biological uptake. 

Finally, annual and decadal changes in precipitation can lead to long-term changes in surface runoff or 

instream dilution, contributing to long-term changes in nutrient concentrations in streams.
40 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

This page intentionally left blank
Chapter 3

Chapter

3 NAWQA’s Approach 

to Nutrient 

Assessment 

Introduction

The NAWQA Program’s assessment of nutrients during 1992–2004 provides one of the most comprehensive 

analyses to date of nutrient occurrence in streams and groundwater of the United States. The assessment 

followed a national study design in which some of the most important hydrologic systems were studied on 

a rotational schedule using nationally consistent sampling and analytical methods. This approach yields 

an understanding of water‐quality conditions in a national context, while also supporting comparisons and 

assessments within and among individual watersheds, aquifers, and geographic regions. By systematically 

relating nutrient occurrence and transport to key factors that control nutrient contamination—such as 

nutrient use and properties, land use, hydrology, and other environmental features—NAWQA provides 

information needed for managing nutrients within the Nation’s diverse land-use and environmental settings.

EXPLANATION

National Water-Quality Assessment Study Units

Study Units sampled from 1992 to 2001

Study initiated in 1991

Study initiated in 1994

Study initiated in 1997

High Plains Regional 

Groundwater Study, 

initiated in 1999
42 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Sampling by NAWQA targeted specific land uses including 

agricultural (top), urban (middle), and undeveloped (bottom) lands.

Targeted Sampling Across the Nation’s Diverse 

Land Uses and Environmental Settings

This report is based primarily on results from NAWQA’s first decade 

of water-quality assessments, which were completed on a rotational 

schedule from 1992 to 2001 in 51 major hydrologic systems across 

the country—referred to as Study Units—as well as in the High Plains 

Regional Groundwater Study, using a nationally consistent study design. 

Assessments were conducted in 20 Study Units during 1992–1995; in 

16 Study Units during 1996–1998; and in 15 Study Units during 1998–

2001. Collectively, the 51 NAWQA Study Units and the High Plains 

Study cover a substantial portion of the Nation’s land area; account for 

more than 70 percent of total water use and more than 50 percent of the 

population served by public water supplies and domestic wells; and are 

representative of the Nation’s diverse landscapes, hydrologic systems, 

ecological resources, and land uses. Water samples were collected from 

selected streams and aquifers through 2004 to assess the effects of 

nutrient enrichment on stream ecosystems and to assess trends in nutrient 

concentrations (Chapters 7 and 8, respectively).

The primary objectives of the NAWQA nutrient assessment were to 

determine: (1) the occurrence and concentrations of nutrients in streams 

(ranging from small streams to large rivers) and groundwater; (2) where 

and when nutrients occur in relation to factors that govern their sources 

and transport in the hydrologic system; (3) whether any nutrients may be 

present at concentrations that could affect human health or aquatic life; 

and (4) how concentrations are changing over time. To address these goals, 

NAWQA employed a targeted assessment focusing on studies of:

• Streams and shallow groundwater in specific, relatively 

homogeneous land‐use and environmental settings to relate nutrient 

occurrence to individual types of nonpoint sources; and

• Streams and major aquifers (regionally extensive aquifers that 

are important groundwater resources for water supply) in areas 

of mixed land uses to evaluate the integrated effects of multiple 

sources of nutrients on their occurrence and concentrations.

Details on the sampling design and analytical methods, as well as 

all data used in this report, are available at: http://water.usgs.gov/nawqa/

nutrients/pubs/circ1350.

For the targeted assessment by land use, streams and shallow 

groundwater were sampled in agricultural and urban areas, and in 

undeveloped areas dominated by forest or rangeland. As described in more 

Photograph by Rand Schaal, Ph.D., pilot and photographer.

Photograph by Lynn Betts, U.S. Department of 

Agriculture, Natural Resources Conservation Service.

Photograph by R.G. Johnson, U.S. National Park Service.
Chapter 3

NAWQA’s Approach to Nutrient Assessment 43

detail below and in the accompanying sidebar, 

Unique Features of the NAWQA Approach, 

streams and groundwater were sampled most 

intensively in agricultural and urban areas 

because of the importance of assessing nutrient 

occurrence in areas with the largest manmade nutrient sources. The agricultural areas 

are diverse in climate, geography, and crop 

types, and span coastal, desert, and temperate 

environmental settings. They include, for 

example, areas dominated by concentrated 

animal feeding operations in the Midwest; fields 

of wheat and other grains in the Great Plains; 

mixed row crops and poultry in the East; and 

rangeland in the Southwest. The areas sampled 

in urban settings primarily were residential, 

typically with low-to-medium population 

densities (300 to 5,600 people per square mile). 

Some commercial or industrial areas also were 

included in the assessments, but point sources 

and extensive industrial and downtown urban 

areas generally were not assessed.

Unique Features of the NAWQA Approach

Water-quality assessments by NAWQA, which is a single program among many local, State, 

and Federal programs, were not designed to address all of the Nation’s water-resource information 

needs and issues. Listed below are several characteristics and limitations of the NAWQA approach 

that are important to consider when interpreting the findings on nutrients presented in this report.

• NAWQA assessments collected extensive data to characterize the hydrologic conditions 

at all stream and groundwater sites in the Study Units. These data are critical for 

understanding the physical and chemical factors that control transport of nutrients 

in the environment.

• NAWQA assessments characterized the quality of the available, untreated water resources, 

and not the quality of drinking water (as would be done by monitoring water from 

water-treatment plants or from household taps). By focusing on the quality of streams and 

groundwater in their present condition (ambient water quality), NAWQA studies complement 

many Federal, State, and local drinking-water monitoring programs.

• NAWQA assessments of nutrients focused primarily on nonpoint sources originating from 

fertilizer application, manure, and atmospheric deposition in agricultural, urban, and other 

land-use settings. Some sites—particularly those downstream from major metropolitan 

areas—also may have been influenced by point sources, such as discharges from 

wastewater-treatment plants.

• NAWQA assessments targeted specific land-use settings that are most extensive or 

important to water quality in a wide range of hydrologic and environmental settings across 

the Nation. This targeted approach gives priority to understanding the most critical factors 

influencing water quality. Extrapolation of local and regional results to national analyses, 

however, requires careful definition of each type of water resource and environmental 

setting for which conclusions are drawn and the use of statistical models to extrapolate 

results to resources that have not been measured. 

• NAWQA assessments did not focus on specific sites with known water-quality problems or 

narrowly defined issues, but rather on the condition of the total resource, including streams 

and groundwater in a wide range of hydrologic and land-use settings across the country.
44 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Sampling Design

The national sampling design for the NAWQA 

Program focuses on a characterization of water-quality 

conditions in streams and groundwater that includes 

consideration of a broad suite of physical and chemical 

characteristics of water, streambed sediments, and 

tissues from aquatic organisms, as well as measures of 

the condition of the algal, macroinvertebrate, and fish 

communities. The national assessment of nutrients is 

based on results from the analysis of 28,466 samples of 

water from streams, and 5,101 samples of groundwater 

from the 51 NAWQA Study Units. 

Stream Water

Water samples were collected at 499 stream 

sites for analysis of nutrients in water (fig. 3-1). The 

samples were collected from streams throughout the 

year, including during both high-flow and low-flow 

periods. Most analyses in this report are based on 

2 years of monthly data for each site. Sampling at a 

subset of sites was more intensive during the time of 

highest runoff and use of agricultural chemicals—

generally weekly or twice monthly for a 4- to 

9-month period. 

Each NAWQA stream site was classified to 

evaluate the potential land-use influences on the 

quality of water sampled. The sites were characterized 

by determining the proportions of each major land 

use within each stream’s contributing watershed. 

Table 3-1 lists the criteria used to classify stream 

sites, and figure 3-1 shows the national distribution 

of these categories for the conterminous United 

States. Streams classified as “mixed land use” drain 

mixtures of two or more land-use settings and do not 

meet the criteria described in table 3-1 for individual 

agricultural, urban, or undeveloped settings. Land‐use 

classifications were adjusted for a small number 

of streams that have watersheds with substantial 

areas that did not contribute streamflow during the 

study period. Most streams that were classified as 

agricultural, urban, or undeveloped also commonly 

have small amounts of other land uses in their 

watersheds. For example, and of particular importance 

to findings for nutrients, many streams classified as 

undeveloped have some agricultural or urban activity 

in their watersheds.

Table 3-1. Each stream sampled by NAWQA was 

classified according to the dominant land uses in its 

watershed.

[Modified from Gilliom and others (2006). The land-use data 

set used for these classifications was an enhanced version of 

the USGS 1992 National Land Cover Data (NLCD) (Nakagaki 

and others, 2007)] 

Land-use 

classification Watershed land-use criteria

Agricultural > 50 percent agricultural land and 

 ≤ 5 percent urban land

Urban > 25 percent urban land and 

≤ 25 percent agricultural land

Undeveloped ≤ 5 percent urban land and 

≤ 25 percent agricultural land

Mixed All other combinations of urban,

agricultural, and undeveloped land

Stream discharge and water-quality samples were collected 

throughout the year. Photograph by U.S. Geological Survey.
Chapter 3

NAWQA’s Approach to Nutrient Assessment 45

17-0191_Fig_3-01_SamplingDesignandNLCDe.ai

Agricultural

Urban

Undeveloped

Mixed

Land-use classification

EXPLANATION

Nationally consistent data not available

for Alaska and Hawaii

Groundwater studies

Mixed land use (94)

Land-use studies of shallow groundwater

Major aquifer studies

NAWQA Study Unit

High Plains Regional 

Groundwater Study

Agricultural (135 sites)

Urban (55)

Undeveloped (159)

Stream-water sampling sites

Mixed land use (150)

Watershed land use

NAWQA Study Unit

Agricultural (53 studies)

Urban (33)

Undeveloped (9)

Figure 3-1. Stream sampling sites and groundwater studies in agricultural, urban, and undeveloped areas were 

distributed across the Nation’s diverse environmental settings to evaluate the occurrence of nutrients within areas of 

specific land uses and in different environmental settings.
46 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Most of the wells sampled as part of land-use studies were new or existing 

observation wells. Photograph by U.S. Geological Survey.

Statistical models that relate nutrient concentrations to 

streamflow and time were used to compute flow-weighted, 

mean annual concentrations of ammonia, nitrate, total 

nitrogen, orthophosphate, and total phosphorus. Use of 

flow-weighted mean annual values facilitates comparisons 

among sites and avoids the potential bias to assessment results 

caused by differences in the number of samples collected at a 

site, sampling frequency, and varying flow conditions during 

the period of sampling. Models were developed to estimate 

nutrient loads and concentrations for each day of the year. 

The models were calibrated using nutrient concentrations 

from stream samples and mean-daily streamflow for the date 

of sampling. These daily values were then used to calculate 

unbiased summary statistics—including mean annual loads, 

yields, and flow-weighted concentrations—which were then 

used to make comparisons among sites.

Groundwater

NAWQA assessed nutrients in groundwater within 

specific land-use settings and in major aquifers influenced by 

a mixture of land uses. Dissolved nutrients were analyzed in 

water samples from 5,101 wells that were part of 189 land-use 

and major aquifer study networks (fig. 3-1). Unlike stream 

monitoring sites, which were sampled multiple times, wells 

were sampled only once because of the comparatively slow 

rates of change of water quality in most groundwater systems 

relative to the rates of change typical of streams. Data analyses 

were based on one sample per well.

Land-use studies focused on shallow groundwater 

primarily within agricultural and urban land-use settings, 

and to a lesser extent in undeveloped areas. Most of the 

wells sampled that were part of land-use studies were new 

or existing observation wells or domestic supply wells. Each 

study involved sampling about 20 to 30 randomly located 

wells within the targeted land-use area. In most of the wells, 

samples were collected from depths less than 20 feet below 

the water table, thus indicating, as directly as possible, the 

influence of each land use on shallow groundwater quality.

Major aquifer studies involved sampling about 20 to 

30 domestic or public-supply wells that withdraw water 

from aquifers or aquifer systems that are important sources 

of water supply. Wells that were sampled for these studies 

were randomly selected throughout the areas underlain by 

each major aquifer, without regard to land use. Thus, the 

groundwater sampled for the major aquifer studies reflects the 

effects of a mixture of different land uses and groundwater 

ages on water quality, often including water that was 

recharged long distances from the sampled wells and in a 

variety of different land-use settings. The nature and extent of 

each major aquifer sampled for these studies is described in 

the summary report for the NAWQA Study Unit in which it 

occurs (see http://water.usgs.gov/nawqa/).

NAWQA also conducted studies that describe the change 

in water quality along a groundwater flow path from the point 

of recharge at the land surface to the point of discharge—

for example a stream or lake in a natural flow system, or a 

pumped well. Design of these “flow‐system studies” was 

tailored to the topic being addressed as well as the specific 

environmental framework at each locale. Examples of topics 

addressed include transport of constituents to drinking-water 

wells, and transport of agricultural chemicals in groundwater 

to streams. 

Groundwater sampled during the NAWQA studies was 

classified into one of three categories of redox condition 

based on the concentrations of several diagnostic constituents 

(Jurgens and others, 2009):

• Oxic—groundwater with concentrations of dissolved 

oxygen greater than 0.5 mg/L. 

• Reduced—groundwater with concentrations of 

dissolved oxygen less than or equal to 0.5 mg/L, and 

containing chemical markers for iron and manganese 

reduction. 

• Mixed—groundwater with concentrations of dissolved 

oxygen greater than 0.5 mg/L and containing chemical 

markers for iron and manganese reduction.
Chapter 3

NAWQA’s Approach to Nutrient Assessment 47

Agricultural

Urban

Undeveloped

Mixed

0

10

20

30

40

50

60

70

NAWQA stream 

sampling sites

U.S. streams Streams with 

drinking-water intakes

Proportion of watersheds,

in percent

NAWQA Stream-Water Assessment in 

a National Context

Consistent with the NAWQA sampling design, which 

was targeted by land use, the nutrient findings discussed 

in this report generally are presented by land-use category. 

Aggregation of NAWQA findings for streams across all 

land-use categories would not accurately represent all 

streams in the conterminous United States (fig. 3-2), which 

were characterized by classifying the watersheds of all 

stream segments in the USEPA River Reach File (Nolan 

and others, 2002) using the land-use criteria in table 3-1. 

For example, nearly 30 percent of the streams sampled by 

NAWQA were agricultural streams, whereas agricultural 

streams represent only about 15 percent of all streams in 

the conterminous United States. Furthermore, as shown 

in figure 3-2, agricultural streams represent only about 

12 percent of all streams with public water-supply intakes. 

There are 1,679 public water-supply intakes on streams across 

the Nation for which land use could be characterized. The 

NAWQA design also over-represented urban streams and 

under-represented undeveloped streams compared with the 

national occurrence of streams in these land-use 

settings (fig. 3-2).

Nutrient concentrations in streams can fluctuate in 

response to changes in precipitation and streamflow (see 

Chapter 2, Nutrient Primer), so information on streamflow 

conditions at the time of sample collection is critical for 

assessing nutrient conditions. Because of the rotational 

sampling design used in the NAWQA assessment and because 

of regional variations in climate, hydrologic conditions during 

the NAWQA sampling periods were not uniform across all 

streams. Instead, regional patterns in climate resulted in many 

eastern streams having normal to above normal flow during 

Figure 3-2. The NAWQA design for stream assessments placed 

greater emphasis on sampling streams that drain agricultural and 

urban watersheds (as defined in table 3-1), relative to those in 

undeveloped watersheds. Streams sampled by NAWQA included 

higher proportions of those classified as agricultural and urban—

and lower proportions of those classified as undeveloped—

compared with all streams in the conterminous United States 

and those with drinking-water intakes. (Modified from Gilliom and 

others, 2006.)

their respective sampling period, whereas flows in western 

streams were variable, with more having below normal flow 

during their sampling period (fig. 3-3). Streamflow also varied 

within the sampling period at many sites. For example, the 

3-year sampling period for the Flint River in Alabama, the 

Great Miami River in Ohio, and the Spokane River in Idaho 

included both wet and dry periods (fig. 3-3). This hydrologic 

variability adds complexity to a comparison of sites by 

geographic region or land use.
48 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

17-0191_Fig_3-03.ai

Flint River near Brownsboro, Alabama

Streamflow, in cubic

feet per second

100,000

10,000

1,000

100

10

1999 2000 2001

Oct

Jan

Apr

July

Oct

Jan

Apr

July

Oct

Jan

Apr

July

75th percentile

25th percentile

based on water

years 1934–1994

Streamflow

wet

dry

Water year

Great Miami River at Hamilton, Ohio

1999 2000 2001

Streamflow, in cubic

feet per second

100,000

10,000

1,000

100

10

Oct

Jan

Apr

July

Oct

Jan

Apr

July

Oct

Jan

Apr

July

75th percentile

25th percentile

based on water

years 1971–2000

Streamflow wet

dry

Water year

Spokane River near Post Falls, Idaho

Streamflow, in cubic

feet per second

50,000

10,000

5,000

500

1,000

100

1999 2000 2001

Oct

Jan

Apr

July

Oct

Jan

Apr

July

Oct

Jan

Apr

July

75th percentile

25th percentile

based on water

years 1970–2001

Streamflow wet

dry

Water year

Departure of streamflow during the 

NAWQA sampling period from the 

long-term mean streamflow (1971 

to 2000), in percent).

Much below normal (≤25)

Below normal (25–75)

Normal (75–125)

Above normal (125–175)

Much above normal (175)

EXPLANATION

Figure 3-3. Streamflow at many eastern stream sites was normal to above normal during their respective sampling 

periods, whereas flows at western stream sites were variable, with more being below normal during their sampling 

period. These contrasts reflect both the rotational sampling design used in the NAWQA assessment and regional 

variations in climate. Streamflow also varied within the sampling period at many sites; samples from the Flint River in 

Alabama (Woodside and others, 2004), the Great Miami River in Ohio (Rowe and others, 2004), and the Spokane River in 

Idaho (Clark and others, 2004) were collected during both wet and dry periods.
Chapter 3

NAWQA’s Approach to Nutrient Assessment 49

Area within 500-meter 

radius of NAWQA 

sampled wells

All U.S. area over

groundwater resource

0

10

20

30

40

50

60

70

Proportion of land area, 

in percent

Agricultural

Urban

Undeveloped

Major aquifers

NAWQA Groundwater Assessment in a 

National Context

NAWQA findings for groundwater, as for streams, are grouped 

by land use in this report. NAWQA’s targeted sampling design for 

groundwater over-represented areas with agricultural, urban, and 

mixed land use, and under-represented undeveloped areas when 

compared with the national distribution of these land-use settings 

overlying known groundwater resources (fig. 3-4). Comparisons 

of land-use distributions for the NAWQA-sampled wells with 

distributions for the entire Nation were based on NAWQA land-use 

classifications (as defined in table 3-1) for every square-kilometer 

area in the conterminous United States. Under‐representation of 

undeveloped areas results from the targeting of agricultural and urban 

areas by the studies of shallow groundwater, and the scarcity of 

water‐supply wells in areas that have little or no human activity. 

Extrapolation to Unsampled Areas

NAWQA assessments use an integrated approach that 

includes both monitoring and modeling. Monitoring provides 

direct observations, often over time, of water-quality properties 

and characteristics, whereas models are tools that help interpret 

these observations. Analysis of model simulations can advance 

understanding of the relation of water quality to human activities and 

natural processes that affect spatial variations in quality. 

Nutrient data collected by NAWQA during its first decade 

support the development and testing of a wide range of models, 

particularly statistical models, that are being used to predict nutrient 

concentrations in streams and groundwater for locations where 

nutrient concentrations have not been measured. This expansion 

of water-quality assessments from individual monitoring sites to 

unstudied locations by use of models for prediction, or spatial 

extrapolation, is fundamental to extending targeted local and regional 

studies to a comprehensive national assessment. 

NAWQA statistical models establish quantitative linkages 

between nutrient concentrations measured at sampling sites with the 

associated explanatory variables that represent sources of nutrients, 

hydrology, and characteristics of soils, geology, and other factors. The 

models are built using the explanatory variables that best correlate 

with, or explain, concentrations of selected nutrients observed in 

streams and groundwater. Although explanatory variables included in 

the models are significantly correlated with nutrient concentrations, 

the specific cause-and-effect relations responsible for the observed 

correlations are not always clear, and inferences regarding causes 

should be considered as hypotheses. Models complement the 

monitoring by helping to estimate the extent of concentrations of 

concern, or by indicating vulnerable areas that can benefit from 

enhanced monitoring and protection. The statistical models are 

constrained to representing areas within the conterminous United 

States because data on nutrient sources and transport factors are 

unavailable for Alaska and Hawaii.

Figure 3-4. NAWQA’s targeted sampling design for 

groundwater emphasized areas with urban, mixed, 

and agricultural land use—and under-represented 

undeveloped areas—when compared with the national 

distribution of land uses. (Modified from Gilliom and 

others, 2006.)

The Spokane River near Spokane, Washington. Photograph by Lan 

Tornes, U.S. Geological Survey.
50 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Development of Models for Total 

Nitrogen Concentrations in Streams

Models developed to extrapolate total 

nitrogen concentrations in streams used linear 

regression statistical techniques to relate 

flow-weighted, mean annual total nitrogen 

concentrations at 462 sites to characteristics 

(explanatory factors) associated with watersheds 

draining streams in the USEPA River Reach File 

(Spahr and others, 2010). The models relate total 

nitrogen concentrations to nitrogen inputs, basin 

characteristics, and hydrologic factors using data 

collected from 1992 to 2001. Optimal results 

were achieved by dividing the sites into two 

groups based on the percentage of agricultural 

land use in the upstream watershed: 220 sites 

referred to as “agricultural” drain watersheds 

with more than 25 percent of agricultural land 

use, and 242 sites referred to as “nonagricultural” 

drain watersheds with less than 25 percent 

agricultural land use. 

The total nitrogen concentration at each 

site was represented by a flow-weighted, 

mean annual concentration to represent the 

movement of nitrogen mass throughout the year. 

After testing numerous potential explanatory 

factors, eight were selected for the model of 

agriculturally influenced sites and four were 

selected for the model of nonagricultural sites. 

The regression models were used to extrapolate 

total nitrogen concentrations to the more than 

600,000 miles of streams depicted in the USEPA 

River Reach File (Nolan and others, 2002). The 

results of simulations made with both models 

were merged to produce a national map that 

shows the predicted mean estimates of the total 

nitrogen concentration. 

Development of the Nonlinear 

Nitrate Models for Groundwater

Two models based on nonlinear regression 

were developed by NAWQA to predict 

nitrate concentrations in groundwater of the 

conterminous United States (Nolan and Hitt, 

2006). The first model uses data primarily from 

monitoring wells to predict nitrate contamination 

of shallow (10 meters, or 33 feet), recently 

recharged groundwater. The second model uses 

data from domestic and public-supply wells to 

predict nitrate contamination in drinking water. 

The median depth of the drinking-water supply 

wells was 50 meters (164 feet). The shallow 

model is intended to maximize correlations with 

overlying land use, whereas the drinking-water 

model represents the used resource.

The models for predicting nitrate 

concentration in groundwater are based on 

averages of nitrate concentration and other 

characteristics of NAWQA groundwater studies. 

The average nitrate concentration of water in 

the wells sampled in each study was used to 

smooth local variability, so that the predominant 

factors that influence nitrate contamination at the 

national scale would be more readily apparent. 

The shallow groundwater model was based on 

data from 97 studies in which most samples 

were collected from monitoring wells, whereas 

the drinking-water model was based on data 

from 111 studies in which all samples were 

collected from domestic or public-supply wells. 

Data used to develop the models were collected 

during 1991–2003 and represent the first full 

decade of sampling by NAWQA. More than 

100 explanatory factors were tested in the models 

to identify those that most reliably predict nitrate 

concentrations in groundwater: 16 factors were 

selected for the shallow groundwater model, and 

14 factors were selected for the drinking-water 

model. Model predictions were made for each 

square-kilometer area in the conterminous United 

States for which a complete suite of input data 

was available, resulting in more than 8 million 

predictions. Uncertainty analysis was performed 

with the final models by varying model equations 

hundreds of times to produce a mean and 

variance of predictions at each groundwater 

study location. 
Chapter 4

Occurrence and 

Distribution of 

Nutrients in 

Streams and 

Groundwater

Introduction

NAWQA’s assessment of nutrients in 

streams and groundwater of the United 

States includes hydrologic systems 

representative of the Nation’s diverse 

landscapes, ecological resources, and 

climatic conditions. The assessment is 

targeted to specific land-use settings that 

are important to water quality across the 

Nation, allowing for characterization 

of the occurrence and distribution 

of nutrients in relation to land use 

and geographic patterns. Results of 

the assessment also can be used to 

identify critical factors influencing the 

occurrence and distribution of nutrients 

in streams and groundwater, such as 

anthropogenic (human) nutrient inputs, 

seasonal variability, and physical and 

chemical aquifer characteristics.

Photograph by Norman Spahr, U.S. Geological Survey.

Chapter

4
52 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Sites with minimal human impact, such as the Colorado River in Rocky Mountain National Park, 

were chosen to represent background nutrient conditions. Photograph by J.R. Deacon, U.S. 

Geological Survey.

Background Conditions

What would nutrient concentrations be in streams and 

groundwater if there were no effects of human development? 

An answer is not readily available for many parts of the Nation 

because human development is so extensive, and remaining 

pristine sites, even where present, are often not monitored. 

To help answer this question, the NAWQA Program collected 

samples from streams and wells, and gathered complementary 

data from other programs, in areas with minimal or no 

development (see sidebar, Estimation of Background 

Concentrations). These samples reflect nutrients that are 

present in streams and groundwater as a result of purely 

natural processes, as well as low-level inputs of nutrients from 

anthropogenic sources such as atmospheric deposition. Data 

from these samples were used to estimate what concentrations 

might be expected under minimally impacted or “background” 

conditions across the United States.

The nutrient concentrations estimated to represent 

national background concentrations are listed in table 4-1. 

Table 4-1. Estimates for national background concentrations of nutrients in streams and groundwater.

[ mg/L, milligrams per liter; –, not applicable]

Data set

Ammonia Nitrate Total Nitrogen Orthophosphate Total Phosphorus

Sites or 

wells

Concentration

(mg/L) 

Sites or 

wells

Concentration

(mg/L) 

Sites or 

wells

Concentration

(mg/L) 

Sites or 

wells

Concentration

(mg/L) 

Sites or 

wells

Concentration

(mg/L) 

Streams 89 0.025 108 0.24 88 0.58 89 0.010 84 0.034

Groundwater 177 0.10 419 1.0 – – 166 0.030 – –

These estimates can be compared with measurements made 

at other locations to determine whether development has 

resulted in elevated concentrations. Nutrient concentrations 

in undeveloped areas may vary considerably among regions 

of the country, but the number of sites sampled is insufficient 

to define small-scale variations. The regional variability in 

background nutrient concentrations is discussed in the context 

of the development of nutrient criteria protective of aquatic 

life in Chapter 7.

In areas of substantial agricultural or urban development, 

nutrient concentrations are likely to be elevated above 

background levels. Flow-weighted mean annual concentrations 

for all five nutrient constituents exceeded the background 

concentrations at 90 percent of 190 NAWQA agricultural and 

urban sites. Median concentrations of nitrate exceeded the 

groundwater background in 64 percent of 86 shallow aquifer 

studies sampled by NAWQA in areas underlying agricultural 

or urban land use; however, concentrations of ammonia and 

orthophosphate were not greater than background levels in 

most areas.
Chapter 4

Occurrence and Distribution of Nutrients in Streams and Groundwater 53

EXPLANATION

Sites used in estimating background

concentrations of nutrients

Streams

Groundwater

Estimation of Background Concentrations

Estimates of background concentrations of nutrients in streams were based on data from 110 sites selected on the 

basis of criteria used by Clark and others (2000) (fig. 4-1).

1. The upstream basin had less than 5 percent urban land and less than 25 percent agricultural land,

2. The site was classified as a reference, forest indicator, or rangeland indicator site by local experts,

3. The basin area was less than 3,000 km2 (1,158 mi2), 

4. Data were sufficient for estimation of flow-weighted mean annual nutrient concentrations, and 

5. If two sites were on the same stream, only the upstream site was included.

Flow-weighted mean annual concentrations (see Chapter 3, NAWQA’s Approach to Nutrient Assessment) of the five 

nutrient constituents at these 110 sites were computed on the basis of several years of samples (see Mueller and Spahr, 

2005, for details). Background concentrations were estimated as the 75th percentile of the flow-weighted means for all 

sites that had adequate data for each constituent. Selection of the 75th percentile to represent background implies that 

these concentrations are exceeded at no more than 25 percent of minimally impacted streams and aquifers.

For groundwater, background concentrations were estimated using data from 322 wells selected on the basis of criteria 

specified by Nolan and Hitt (2003), and data from an additional 97 wells sampled by NAWQA during 1999–2001 that fit the 

same criteria (fig. 4-1). Background concentrations were estimated as the 75th percentile of a single representative sample 

from each of the 419 wells that had data for the nutrient in question. Only dissolved constituents were included because 

particulate nitrogen and phosphorus are negligible in groundwater.

Figure 4-1. Nutrient data from 110 stream sites and 419 wells in relatively undeveloped areas were used to 

estimate minimally impacted (background) concentrations for the United States.
54 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

Concentrated animal feeding operations, also referred to as “CAFOs,” are potential sources of nutrients to streams and 

groundwater. Photograph by Jeff Vanuga, U.S. Department of Agriculture, Natural Resources Conservation Service, 2002.

Nutrient Concentrations in Streams 

Relations to Land Use

Variations in the occurrence and distribution of 

nutrients in streams reflect, in part, differences in land use 

and associated nutrient sources. Nonpoint inputs, such as 

those from fertilizers and manure from livestock, are the 

major sources of nutrients in agricultural areas, whereas 

both point and nonpoint sources—including wastewater 

effluent from municipal or industrial facilities; fertilizers 

applied to lawns, golf courses, and parks; septic systems; and 

atmospheric deposition—are the major sources in urban areas. 

In undeveloped areas, nonpoint inputs, such as atmospheric 

deposition and natural sources released by weathering of rocks 

and soil, typically are the largest sources. NAWQA sampling 

sites in watersheds were classified by land use: agricultural, 

urban, mixed, and undeveloped (see Chapter 3, NAWQA’s 

Approach to Nutrient Assessment, table 3-1). Urban sites were 

selected to avoid the effects of major wastewater-treatment 

plants and other point sources, but in some locations this was 

not feasible. 

Median flow-weighted nutrient concentrations for all 

constituents were higher in streams in developed areas—that 

is, agricultural, urban, or mixed land-use streams—than in 

streams in undeveloped areas (fig. 4-2). Concentrations of 

total nitrogen were higher in agricultural streams than in 

streams with urban, mixed, or undeveloped land use, with a 

median concentration of 3.8 mg/L—about 6 times greater than 

background levels. Concentrations of total nitrogen in urban 

streams were lower than those in agricultural settings, with a 

median concentration of 1.5 mg/L (about 3 times greater than 

background levels). Concentrations of total phosphorus were 

similarly elevated in streams in both agricultural and urban 

areas, with median concentrations of 0.26 and 0.25 mg/L, 

respectively—again about 6 times greater than background 

levels. Concentrations of ammonia and orthophosphate were 

similar in agricultural, urban, and mixed land-use streams. 

In urban and mixed land-use streams, the relatively higher 

concentrations of ammonia, orthophosphate, and total 

phosphorus compared to concentrations of nitrogen likely 

were due to the influence of point sources; many of the highest 

concentrations occurred at sites downstream from wastewatertreatment plants. Although samples from undeveloped streams 

had lower concentrations of total phosphorus than samples 

from streams in other land uses, the contrast was not as great 

as for other nutrients. The likely cause is naturally occurring 

phosphorus associated with the high suspended-sediment 

concentration in some undeveloped streams.
Chapter 4

Occurrence and Distribution of Nutrients in Streams and Groundwater 55

17-0191_Fig_4-02_sw_boxplot_landuse.ai

90th percentile

10th percentile

Median

75th percentile

25th percentile

EXPLANATION

Background concentration

0.025

Concentration, in milligrams per liter

0

2

4

6

8

10

12

Total nitrogen

Agricultural Urban Mixed Undeveloped

Nitrate

0.58

Concentration, in milligrams per liter as P Concentration, in milligrams per liter

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.0

0.2

0.4

0.6

0.8

1.0

1.2

0.24

0.034

Agricultural Urban Mixed Undeveloped

Orthophosphate

Agricultural Urban Mixed Undeveloped

0.010

Concentration, in milligrams per liter as N

0

2

4

6

8

10

12

Agricultural Urban Mixed Undeveloped

Ammonia

Concentration, in milligrams per liter as N 

Agricultural Urban Mixed Undeveloped

0.025

0.0

0.1

0.2

0.3

0.4

0.5

Total phosphorus

Figure 4-2. In streams, concentrations of total nitrogen and nitrate were higher in agricultural streams than in urban 

or mixed land-use streams, whereas concentrations of ammonia, orthophosphate, and total phosphorus were similar in 

agricultural, urban, and mixed land-use streams.
56 Nutrients in the Nation’s Streams and Groundwater, 1992–2004

1

2

3

4

5

6

7

8

Geographic framework used in 

discussion of nutrients in streams

and groundwater

1—Northeast 

2—Southeast 

3—Midwest 

4—Northern Plains 

5—Southern Plains 

6—Southwest 

7—Northwest 

8—California 

EXPLANATION

(New England and Mid-Atlantic Water-Resources Regions)

(South Atlantic-Gulf and Tennessee Water-Resources Regions)

(Great Lakes, Ohio, Upper Mississippi, and Souris-Red-Rainy Water-Resources Regions)

(Missouri Water-Resources Region)

(Lower Mississippi, Arkansas-White-Red, and Texas-Gulf Water-Resources Regions)

(Rio Grande, Upper Colorado, Lower Colorado, and Great Basin Water-Resources Regions)

(Pacific Northwest Water-Resources Region)

(California Water-Resources Region)

Geographic Distribution

The geographic distribution of nutrients in streams 

reflects regional differences in nutrient sources, hydrologic 

characteristics of watersheds, and chemical and biological 

processes that affect specific nutrients. In this section, 

interactions among these factors are illustrated by comparing 

the geographic distributions of total nitrogen and total 

phosphorus in streams. The comparisons are illustrated using 

a series of national maps showing the relative range (high, 

medium, or low) of concentrations for sites downstream 

Geographic Framework 

Describing the geographic distribution of nutrients requires a spatial framework with a defined terminology to delineate 

different areas. For the purposes of this report, the continental United States was divided into eight contiguous areas 

on the basis of water-resources regions (fig. 4-3). Seaber and others (1987) used the boundaries of major river basins to 

define 21 water-resources regions. The areas designated on the map below are either single water-resources regions or 

combinations of regions. These area designations are used in the discussion of geographic distribution of nutrients in streams 

and groundwater. Alaska and Hawaii are individual regions.

Figure 4-3. For the purposes of this 

report, the continental United States 

was divided into eight contiguous areas 

that are based on water-resources 

regions. These area designations are 

used in this report in the discussion of 

geographic distribution of nutrients in 

streams and groundwater.

from specified land uses (fig. 4-4) (see sidebar, Geographic 

Framework). Sites at which concentrations were within the 

lowest 25 percent of the data are shown in the “Low” range, 

sites where concentrations were within the upper 25 percent of 

the data are shown in the “High” range, and all other sites are 

shown in the “Medium” range. The background shading on the 

maps identifies nonpoint-source input rates of nitrogen 

and phosphorus.