U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2013–3033

July 2013

Aquatic biological communities, which are collections of organisms, are a direct measure of stream health because they 

indicate the ability of a stream to support life. This fact sheet highlights selected findings of a national assessment of 

stream health by the National Water-Quality Assessment (NAWQA) Program of the U.S. Geological Survey (USGS). The 

assessment was unique in that it integrated the condition of three biological communities—algae, macroinvertebrates, 

and fish—as well as measures of streamflow modification, pesticides, nutrients, and other factors. At least one biological community was altered at 83 percent of assessed streams, and the occurrence of altered communities was highest in 

urban streams. Streamflows were modified at 86 percent of assessed streams, and increasing severity of streamflow modification was associated with increased occurrence of altered biological communities. Agricultural and urban land use in 

watersheds may contribute pesticides and nutrients to stream waters, and increasing concentrations of these chemicals 

were associated with increased occurrence of altered biological communities.

At least one biological community—algae, macroinvertebrates, 

or fish—was altered in 83 percent of assessed streams. 

The occurrence of altered biological communities was 

higher in urban than agricultural settings (89 percent versus 

79 percent of assessed sites, fig. 1). All three communities—

algae, macroinvertebrates, and fish—were altered in 22 percent

of assessed streams. A biological community was classified as

altered at a stream site if the numbers and types of organisms

in it were substantially different from its natural potential as

estimated from regional reference sites. The high occurrence of

altered communities suggests that stream health is threatened by

a wide variety of land and water use across the Nation.

Figure 1. Regardless of the land-use setting, at least one biological community was altered, relative to regional reference conditions, at 

83 percent of the streams where integrated assessments of algal, macroinvertebrate, and fish communities were conducted.

unaltered

altered

21%

79%

unaltered

altered

11%

89%

unaltered

altered

17%

83% altered

All sites

17%

83%

unaltered

Number of altered 

communities

none

1

2

3

Mixed use

Agricultural Urban

167 sites 114 sites

304 sites

The Quality of Our Nation’s Waters

Ecological Health in the Nation’s Streams
Unaltered biological communities were present in 17 percent 

of assessed streams.

The presence of unaltered biological communities in 

agricultural and urban watersheds suggests that it is possible 

to maintain stream health despite substantial human activities 

in a watershed. Within each land-use setting, altered biological

communities varied widely in the degree to which they differed from their natural potential. This finding suggests that the

effects of agricultural and urban land use on stream health are 

not uniform across the Nation, but depend on factors such as

local land-use practices, climate, and topography.

Assessments limited to a single biological community are 

likely to underestimate the influence of land and water use 

on stream health.

Integrated assessments of algal, macroinvertebrate, 

and fish communities revealed twice as many altered streams

in agricultural and mixed-use settings compared to singlecommunity assessments. Multicommunity assessments increase

the likelihood of detecting reduced stream health because 

species in different communities have unique vulnerabilities to 

manmade changes in their physical and chemical surroundings.

Reduced stream health is associated with manmade 

modifications to physical and chemical factors that 

often result from land and water use.

Maintenance of stream health requires that

physical and chemical properties of streams remain

within the bounds of natural fluctuations. Many

naturally occurring species have low tolerances

to changes in their physical or chemical environment. When physical and chemical properties of

streams are shifted beyond their natural ranges,

vulnerable species may be eliminated, ultimately

reducing stream health.

Manmade modifications to key physical and

chemical factors that control stream health are 

extensive, occurring in all types of land-use settings.

Recent assessments by NAWQA, the U.S. Environmental Protection Agency, State agencies, and others

have documented the importance of habitat modification, chemical contaminants, and nonnative species 

in reducing stream health across the Nation. This

fact sheet focuses on the importance of modified flows, excess

nutrients, and pesticides to the health of streams and rivers.

Streamflow Modification

Annual high or low flows were modified in 86 percent of

the streams assessed across the Nation (fig. 2). Natural fluctuations of flows are critical to stream health because they build

and maintain physical habitats, influence physical and chemical

characteristics of water, and provide important life-stage cues

for aquatic organisms. Streamflows are modified by a variety

of land- and water-management activities, including reservoir

storage and releases, stream diversions, subsurface tile drainage, 

groundwater withdrawals, wastewater inputs, and removal of 

vegetated land cover in the watershed.

Biological communities were altered more frequently in

streams with modified flows. The occurrence of altered fish

communities increased 12–40 percent in streams with increasing severity of depleted high flows (fig. 3). This association

between biological alteration and streamflow modification was

evident even after controlling for the influence of other factors

that affect biological communities, such as nutrients, salinity,

and land cover (Carlisle and others, 2010).

Figure 2. Annual high or low streamflows were 

modified in 86 percent of assessed stream sites. 

Streamflow modification was either depleted (less 

than) or inflated (greater than) relative to expected 

natural magnitudes. Although high flows were depleted 

throughout the United States, low flows tended to be 

depleted in arid regions and inflated in wet regions. These 

results highlight the value of long-term streamflow data collected 

by the USGS in cooperation with numerous local, State, and Federal 

partners across the Nation.

inflated

unaltered

depleted

Annual high flow

Annual low flow

Arid

Wet

2
Excess Nutrients

Excess concentrations of nutrients (also known as “nutrient enrichment”) are widespread in the Nation’s streams

(Dubrovsky and others, 2010; U.S. Environmental Protection

Agency, 2013). A variety of sources can contribute nutrients to

streams, such as wastewater and industrial discharges, fertilizer 

and manure applications to agricultural land, runoff from urban 

areas, and atmospheric sources. Nutrient sources and resulting

concentrations in streams vary across the Nation on the basis

of regional differences in agricultural practices, urban land use, 

and natural factors such as climate and geology (Dubrovsky and

others, 2010).

With increasing nutrient enrichment in stream water, the

occurrence of altered algal communities increased from 21 to

39 percent (fig. 4). Biological alteration associated with elevated

45

40

35

30

25

20

15

10

5

0

Severity of depleted high flows,

in percent reduction from natural

25–50% 51–75% 76–100%

Low Moderate High

Increased occurrence of altered

communities, in percent above baseline

Altered fish communities

Nutrient enrichment, 

in milligrams per liter of total nitrogen

Altered algal communities

Increased occurrence of altered

communities, in percent above baseline

 Moderate High

40

35

30

25

20

15

10

5

0

0.7–1.5 > 1.5

Figure 4. The 

occurrence of 

altered biological 

communities 

increased in streams 

with greater nutrient 

enrichment—a 

pattern that was 

most pronounced for 

algal communities. 

nutrient levels was most pronounced for algal communities, 

likely because of the direct link between nutrient availability

and algal growth and reproduction. Alteration of algal communities is typified by changes in the types of algae—such as diatoms—that are predominant in a stream. Some types of diatoms

thrive in streams with elevated nutrients and are referred to as 

“eutrophic diatoms.” These species were a predominant part of

algal communities in streams with elevated nutrients throughout 

the Nation (fig. 5). Deleterious effects to aquatic animals occur

when excess nutrients cause excessive growths of algae and 

other aquatic plants, which consume oxygen in the water as they

grow, die, and decompose. These effects, however, can vary

from one stream to another as a result of differences in streamflow, amount of riparian shading, and water clarity (Dubrovsky

and others, 2010).

Figure 5. Eutrophic diatoms—a type of algae that prefer elevated nutrients—are a predominant part of algal communities 

across the Nation, particularly in regions with relatively high amounts of nutrient application such as the Corn Belt and 

irrigated agricultural lands in the West (from Dubrovsky and others, 2010). 

Estimated 1997 nitrogen inputs from 

fertilizer, manure, and atmosphere, 

in pounds per square mile

<2,900

2,900–15,000

>15,000

Percentage of eutrophic diatoms

0.0–3.5

>3.5–12.7

>12.7–31.0

>31.0–89.5

Baseline for graph was established from 

streams with minimal or no streamflow modification. Results were similar for modification 

of low flows.

Baseline for graph was established from 

streams with comparatively low (<0.7 milligram 

per liter) total nitrogen. Results were similar for 

total phosphorus.

3

Figure 3. The occurrence 

of altered fish communities 

increased in streams with 

increasingly depleted 

high flows. Reservoirs, 

diversions, and other 

manmade changes 

to streams and their 

watersheds modify natural 

streamflows that are 

critical to the life stages of 

aquatic animals.
Pesticides

Pesticides are detected in stream water in all land-use

settings and typically reflect patterns of use in the watershed

(Gilliom and others, 2006). Although pesticide concentrations

are highly variable seasonally and from year to year, they may

reach levels that are potentially harmful to biological communities, particularly in agricultural and urban streams (Gilliom and

others, 2006).

The occurrence of altered macroinvertebrate communities increased from 20 to 42 percent in streams with greater

potential toxicity of pesticide mixtures (fig. 6). This association

is expected because stream macroinvertebrate communities are 

mainly composed of insects, and the most frequently detected—

and potentially toxic—pesticides were insecticides (chlorpyrifos, carbaryl, and diazinon), which are designed to kill insects.

After controlling for nutrients, salinity, habitat, and land use,

streams with insecticide levels that exceeded aquatic-life benchmarks had 12 percent fewer macroinvertebrate taxa than streams

without insecticide exceedances (Yuan and others, 2009). These

findings suggest that pesticides contribute to reduced stream

health in agricultural and urban streams, and support a growing 

body of literature documenting the adverse effects of pesticides

on aquatic biological communities.

Biological communities 

inhabiting streams include 

algae, macroinvertebrates, 

and fish. Integrated 

assessments of multiple 

communities provide 

the most comprehensive 

measure of stream health 

because each community 

has important roles in the 

ecosystem and unique 

vulnerabilities to manmade 

changes in their physical and 

chemical surroundings. 

Figure 6. The occurrence of altered 

macroinvertebrate communities increased in 

streams where potential toxicity of dissolved 

pesticide mixtures was higher. Concentrations 

of widely used insecticides often occur in 

stream water at levels that are harmful to 

macroinvertebrate communities, which are 

dominated by aquatic insects. Baseline for 

graph was established from 132 streams 

where no pesticides were detected. 

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 Drawing by Frank Ippolito, http://www.productionpost.com

Intermediate High

Potential toxicity of dissolved 

pesticide mixtures

Increased occurrence of altered

communities, in percent above baseline

Altered macroinvertebrate 

communities

45

40

35

30

25

20

15

10

5

0

Low
5

Management Implications

•	 Assessments that are limited to a single biological community are likely to underestimate the effects of land 

and water use on stream health. 

•	 Water quality is not independent of water quantity because flows are a fundamental part of stream health. 

Because flows are modified in so many streams and rivers, there are many opportunities to enhance stream 

health with targeted adjustments to flow management.

•	 Efforts to understand the causes of reduced stream health should consider the possible effects of nutrients 

and pesticides, in addition to modified flows, particularly in agricultural and urban settings.

•	 Stream health is often reduced due to multiple physical and chemical factors. Understanding how these multiple factors influence biological communities is essential in developing effective management strategies 

aimed at restoring stream health.

Scientists and managers often become 

environmental detectives when assessments indicate that stream health is diminished. They must 

determine which physical or chemical factors 

have been modified by human activities sufficiently 

to alter biological communities. This information is 

essential to developing appropriate management 

strategies. An example from Shingle Creek, an 

urban stream in Minnesota, is presented here.

Chloride concentrations often exceed the aquatic-life benchmark 

during the winter, when salt is applied to roadways in the watershed.

Stream Water Salinity (Chloride)

800

600

400

200

0

Month

Chloride concentration,

in milligrams per liter

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

 Aquatic-life benchmark (chronic)

Dissolved-oxygen concentrations vary widely and often fall below 

State guidelines for the protection of aquatic life during summer 

when algae and other plant growth is highest.

Streamflow is often more variable than would naturally occur, 

indicating the potential for degradation of habitat for many aquatic 

species.

Dissolved Oxygen

Variability of Streamflows 2.5

2.0

1.5

1.0

0.5

0

1998 2000 2002 2004 2006 2008 2010

Year

Coefficient of variation of daily flows

range of natural variability

Year

16

14

12

10

8

6

4

2

Dissolved-oxygen concentration,

0

in milligrams per liter

1996 1997 2000 2002 2004 2006 2010

Minimum benchmark for cool-warm water streams

Algal, macroinvertebrate, and fish communities were 

altered more than 50 percent from baseline conditions.

100

80

60

40

20

0

Algae MacroinvertebratesFish

Biological alteration,

in percent from baseline

Biological Alteration

Unraveling the effects of multiple factors on stream health

Shingle Creek, Minnesota

Algal, macroinvertebrate, and fish communities were severely altered in Shingle Creek, 

indicating poor stream health. Salinity—which 

frequently exceeds aquatic-life benchmarks during 

the winter—was originally thought to be the main 

cause. Followup investigations of other potential 

factors, however, showed that dissolved oxygen 

is often reduced and that streamflows fluctuated 

far beyond natural bounds, which is evidence that 

these factors also contribute to poor stream health. 

As a result of assessing multiple factors, managers now understand that improving the health of 

Shingle Creek requires remediation of several 

important physical and chemical factors.
References

Carlisle, D.M., Wolock, D.M., and Meador, M.R., 2010,

Alteration of streamflow magnitudes and potential ecological consequences: A multiregional assessment: Frontiers in

Ecology and the Environment, v. 9, p. 264–270.

Dubrovsky, N.M., Burow, K.R., Clark, G.M., Gronberg, J.M.,

Hamilton P.A., Hitt, K.J., Mueller, D.K., Munn, M.D., Nolan,

B.T., Puckett, L.J., Rupert, M.G., Short, T.M., Spahr, N.E.,

Sprague, L.A., and Wilber, W.G., 2010, The quality of

our Nation’s waters —Nutrients in the Nation’s streams

and groundwater, 1992–2004: U.S. Geological Survey

Circular 1350, 174 p.

Gilliom, R.J., Barbash, J.E., Crawford, C.G., Hamilton, P.A.,

Martin, J.D., Nakagaki, N., Nowell, L.H., Scott, J.C.,

Stackelberg, P.E., Thelin, G.P., and Wolock, D.M., 2006,

Pesticides in the Nation’s streams and ground water,

1992–2001: U.S. Geological Survey Circular 1291, 172 p.

For Additional Information

Carlisle, D.M., Meador, M.R., Short, T.M., Tate, C.M.,

Gurtz, M.E., Bryant, W.L., Falcone, J.A., and Woodside,

M.D., 2013, Ecological health in the Nation’s streams,

1993–2005: U.S. Geological Survey Circular 1391.

Articles, posters, and a video describing the USGS assessment of the ecological health in the Nation’s streams are

available at http://water.usgs.gov/nawqa/ecology/pubs/

cir-1391/.

6

Assessment Tools

Improving assessments of stream health

U.S. Environmental Protection Agency, 2013, National rivers and

streams assessment, 2008–2009: A collaborative survey, Draft:

U.S. Environmental Protection Agency, Office of Wetlands,

Oceans and Watersheds; Office of Research and Development,

EPA/841/D-13/001, 110 p., accessed May 8, 2013, at

http://water.epa.gov/type/rsl/monitoring/riverssurvey/upload/

NRSA0809_Report_Final_508Compliant_130228.pdf.

Yuan, L.L., Pollard, A.I., and Carlisle, D.M., 2009, Using propensity scores to estimate the effects of insecticides on stream

invertebrates from observational data: Environmental Toxicology and Chemistry, v. 28, p. 1518–1527.

By Daren M. Carlisle and Michael D. Woodside

National Aquatic Bioassessment 

Database

The USGS BioData Retrieval

System provides access to biological

community and physical habitat data

collected by USGS scientists from

streams across the Nation. Data

from more than 15,000 fish, aquatic

macroinvertebrate, and algal community samples can be accessed at

https://aquatic.biodata.usgs.gov/.

National Reference Site Database

The USGS and the Western

Center for Monitoring & Assessment

of Freshwater Ecosystems compiled

biological data from reference-quality

sites across the Nation. These data can

be accessed at http://www.cnr.usu.edu/

wmc/htm/data.

Diatoms of the United States

This online taxonomic guide and 

ecological resource provides identification information about diatoms of 

the United States. Expert contributors

continue to add taxonomic information 

to the database, including high-quality

images, morphological descriptions, 

and key features of each species. For

many species, environmental response

plots and geographic distribution maps 

are also included. This guide can be

accessed at http://westerndiatoms.

colorado.edu. 

Diatoms, a group of mostly single-celled,

microscopic algae, are abundant in nearly

every habitat where water is found—oceans,

lakes, streams, and soils.

Photo by Sarah Spaulding, USGS