National Water-Quality Assessment (NAWQA) Program

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Ecological Health in the Nation's Streams, 1993-2005

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Frequently Asked Questions


Overview of the NAWQA Study Design

National Assessments of Physical and Chemical Factors that Influence Stream Health

Biological Condition Assessment

Factors Associated with Diminished Biological Condition

Implications of Findings of this Study

Priorities for Filling Information Gaps

Supporting Information for this Study

More information on NAWQA and other studies


Who conducted the study?

This study, “Ecological Health in the Nation’s Streams,” was conducted by scientists from the U.S. Geological Survey (USGS) as part of the National Water-Quality Assessment (NAWQA) Program.

What is ecological health and why is it important?

Ecological health (or “stream health”) is the result of the interaction of the biological, physical, and chemical components of the stream ecosystem. Stream health is intact if (1) its biological communities (such as algae, macroinvertebrates, and fish) are similar to what is expected in streams under minimal human influence and (2) the stream’s physical attributes (such as streamflow) and chemical attributes (such as salinity) are within the bounds of natural variation. Naturally functioning streams support countless species—which adds to the Nation’s biological diversity—and provide a wealth of services to society, including water purification, flood control, nutrient recycling, waste decomposition, fisheries, and aesthetics.


What was the purpose of this study?

The objectives of this biological assessment were to: (1) determine the health of streams--based on measures of biological condition of aquatic communities—in agricultural, urban, and mixed land-use watersheds; and (2) investigate how land and water use influence the chemical and physical factors that affect biological condition and ultimately stream health. Streams in this study are defined as being wadeable.


Overview of the NAWQA Study Design

Why did NAWQA use biological condition as a measure of ecological health?

The quality of streams and rivers is often assessed with measures of the chemical or physical properties of water. However, a more comprehensive perspective is obtained if resident biological communities are also assessed. Biological communities provide additional crucial information because they live within streams for weeks to years and therefore integrate through time the effects of changes to their chemical or physical environment. In addition, biological communities are a direct measure of stream health—an indicator of the ability of a stream to support aquatic life. Thus, the condition of biological communities, integrated with key physical and chemical properties, provides a comprehensive assessment of stream health.


Why did NAWQA use more than one biological community to assess biological condition?

Algae, macroinvertebrate, and fish communities provide unique and complementary information to assessments of biological condition and are most often evaluated in water-quality assessments by local, state, and federal authorities. Each of these communities represents a different functional role in the stream, responds in different ways to man-made environmental change, and thus provides different and complementary perspectives on water quality and stream health. Algae have short life cycles of days to weeks and can respond relatively rapidly to changes in water chemistry. Macroinvertebrates are sensitive indicators of changes in water quality or habitat because they inhabit streams from weeks to months. Fish are indicative of water quality across river networks because their longer life cycle which spans years and their ability to swim long distances.


How does NAWQA assess condition of biological communities?

Information about the composition of stream biological communities can be used to assess the degree to which biological communities differ from a natural state. In the NAWQA study, biological condition was assessed by comparing observed (O) community characteristics (such as the number of different types of organisms or taxa) to those expected (E) if the community was minimally disturbed by human activities. Although observed condition (O) was derived from a sample collected at a site, expected (E) condition was estimated with data from a set of environmentally similar reference sites. Because natural variation in environmental settings is accounted for in this approach, departures of observed condition from expected condition are likely the result of human activities.


Is the quality of reference sites used to assess natural or expected conditions the same across the nation?

No. Biological reference sites are needed to establish a baseline or expectation in most biological assessments. Few, if any, streams are totally unaffected by human activities, particularly considering historical disturbances. The level of historic disturbance varies widely across the country. For example, biological reference sites closely approximate pristine conditions in areas that are within protected wilderness, parks, and nature preserves. In contrast, biological reference sites in the Midwest are in watersheds that historically experienced intensive transformations from prairie to farmland, but are currently among the least-disturbed watersheds in that region--such as those with protected riparian buffers (streamside trees and plants). Thus, reference sites used in this assessment are in reality considered least-disturbed or potentially best attainable given the current degree of human influence on the Nation’s landscapes (Stoddard and others 2006) .


How does NAWQA define an “agricultural”, “urban”, and “mixed- use” stream site in their targeted monitoring design?

The NAWQA approach targeted specific land-use settings (agriculture, urban, and mixed-use) among the diverse natural settings across the Nation. “Agricultural” streams drain watersheds that contain greater than 50 percent agricultural land and less than 5 percent urban land. The agricultural streams sampled are diverse in climate, geography, and crop types, and span coastal, desert, and temperate environmental settings. Agricultural settings included, for example, areas dominated by production of corn in the Midwest; wheat in the Great Plains; poultry in the east; pineapple in Hawaii; and vegetables in California.

“Urban” streams drain watersheds that contain greater than 25 percent urban land and less than 25 percent agricultural land. The urban settings studied were primarily residential, typically with low-to-medium population densities (300 to 5,600 people per square mile).

“Mixed use” streams drain watersheds that contain a mix of two or more land uses and do not meet the criteria for individual agricultural or urban settings. Mixed-use streams range in their intensity of development, including some that are influenced by large amounts of agricultural and urban land (draining greater than 50 percent of agricultural land and 25 percent of urban land), and some with little agricultural or urban development.


How does the NAWQA design and sampling-site selection differ from a probabilistic-monitoring design?

NAWQA uses a "targeted" monitoring design in which sites are not selected randomly, but represent certain human activities, land uses, environmental settings, or hydrologic conditions. Such monitoring is useful to answer questions related to water-quality conditions and the natural and human factors that cause those conditions. This approach is different than probabilistic monitoring, which involves random selection of sites across a certain geographic area and sampling each site once during seasonal (spring or summer) low-flow conditions. Such monitoring is useful for getting an unbiased, broad geographic snapshot of "whether or not there is a problem" and "how big the problem is." Probabilistic monitoring and more "targeted" monitoring (such as by NAWQA) answer different types of questions and provide different types of information that are both critical for understanding the ambient resource


Where and when was this study done?

NAWQA assessments of biological condition were conducted on a rotational schedule in 51 major river basins across the United States (referred to as Study Units) from 1993-2005. Collectively, the 51 NAWQA Study Units cover a substantial portion of the Nation’s land area, accounting for more than 70 percent of total water use and spanning a wide range of hydrologic and environmental settings. Such an approach gives priority to understanding the chemical and physical factors— natural and man-made—affecting stream health in diverse environmental settings.

Are streams sampled by the NAWQA study representative of all streams in the conterminous United States?

No. Aggregation of NAWQA findings for streams across all land-use categories would not accurately represent all streams in the conterminous United States. By design, NAWQA’s assessment over-represented urban and agricultural streams and under-represented all other land uses, relative to their occurrence throughout the conterminous United States. For example, urban streams represent about 1 percent of all streams in the conterminous United States, but represent nearly 10 percent of the sites sampled by NAWQA. Agricultural streams represent less than 20 percent of all streams in the conterminous United States, but represent about 30 percent of the sties sampled by NAWQA.

How many streams were sampled for biological communities?

NAWQA’s assessments of algae, macroinvertebrates, and fish were derived from samples collected at 1,976, 1,993, and at 1,242 stream sites, respectively, using published methods ( Samples of all three communities were collected at 1,062 stream sites.

How many streams were sampled for chemical and physical factors?

A wide variety of water chemistry and physical measurements were made at sites where biological communities were sampled. Chemical sampling of water included analyses of nutrients (1,504 sites), major ions (1,309 sites), dissolved pesticides (593 sites), and contaminants associated with streambed sediments (414 sites). All chemical samples were analyzed at the National Water-Quality Laboratory, Denver, Colorado. All field and laboratory protocols are available at:

Physical factors included conductivity (1808 sites), continuous water temperature for a summer (2,149 sites), annual streamflow (2,888 sites with USGS gaging stations plus 1059 hydrologic reference sites), and, daily streamflows were monitored for at least 5 years prior to assessments of algae, macroinvertebrate, and fish condition at 283, 274, and 237 sites, respectively.

Measures of physical habitat were also made at 920 sites where biological condition was assessed. Habitat measurements included the characterization of channel morphology, substrate types, riparian canopy, water depth and velocity using published methods (


National Assessments of Physical and Chemical Factors that Influence Stream Health

How are physical and chemical factors linked to stream health?

Reduced stream health is often associated with man-made changes to the physical (for example, streamflow, water temperature, removal of streamside trees) and chemical (for example, salinity, nutrients, and pesticides) properties of streams. The presence and abundance of species in a biological community are a function of the natural requirements of each species for specific ranges of physical and chemical conditions. If changes in land and water use in a river basin cause physical or chemical properties of streams to exceed their natural ranges, vulnerable aquatic species are eliminated, ultimately reducing biological condition and stream health.


How were physical and chemical factors assessed?

Streamflow modification was assessed at 2,888 sites with USGS gaging stations by comparing observed magnitudes of annual (1980-2007) high and low flows to those expected in the absence of man-made disturbances in the watershed. Expected flows were estimated for each assessed site with statistical models developed from a set of 1059 hydrologic reference sites (Falcone and others 2010; Carlisle and others, 2011).

Water temperature modification was assessed at 2,149 stream sites where continuous monitoring had been conducted for at least one summer during 1999-2009. The observed summertime mean temperature at each site was compared to an expected natural temperature, which was estimated from statistical models (Hill and others, 2013) similar to those used for assessing streamflow modification.

Stream-side trees and other natural vegetation , collectively are known as riparian zones. A national map of agricultural and urban land cover adjacent to streams and rivers was developed using 2006 National Land-Cover Data Set. Riparian zones were defined as all lands within 100 meters of streams. Importantly, this measure of riparian disturbance does not account for activities such as grazing and logging, which can also disrupt riparian zones.

Sampling sites were considered to have elevated salinity if measured conductivity exceeded regional background levels established in a recent national assessment (Van Sickle and Paulsen, 2008). This NAWQA study evaluated 1808 sites where conductivity and biological communities were concurrently sampled.

Nutrient concentrations in stream water were compared to “background concentrations” determined by the NAWQA program (Dubrovsky and others, 2010).

Pesticide concentrations in stream water were compared to water-quality benchmarks available at the time of study (Gilliom and others, 2006). Further, the potential toxicity of dissolved pesticide mixtures was estimated using a pesticide toxicity index (PTI) ( Munn and others, 2006; Gilliom and others, 2006). The index accounts for the concentration of each compound, the relative toxicity of each compound, and the possibility that multiple compounds have additive effects on aquatic organisms. Importantly, the PTI does not measure actual toxicity, but is an index of potential toxicity--the higher the PTI value, the greater the potential toxicity of each compound and the possibility that multiple compounds have additive effects on aquatic organisms.

Contaminants concentrations in stream bed sediments were compared to aquatic-life benchmarks for pesticide compounds. In addition, an index of relative potential toxicity derived from consensus-based freshwater sediment quality guidelines was used to assess the potential effects of sediment contaminant mixtures on biological condition (MacDonald and others 2000). Each contaminant in a sample is divided by its respective sediment quality guideline (SQG), which is the concentration above which toxic effects are expected based on laboratory toxicity tests. The mean SQG provides a basis for screening whether sediment samples are toxic to aquatic life (Long and others, 2006).

How does land and water management influence the physical and chemical properties of streams at the national scale?

Annual low or high streamflows were modified in 86 percent of the 2,888 assessed streams demonstrating that land use and water management have markedly changed natural streamflows across the conterminous United States. The magnitude of low streamflows was modified in 75 percent of assessed stream sites, and the magnitude of high streamflows was modified in 54 percent of assessed sites--resulting in a total of 86% of assessed streams having modified low flows or high flows or both. Streamflow modification was either depleted (less than) or inflated (greater than) relative to expected natural magnitudes. Although high flows were depleted (less than expected) throughout the U.S., low flows tended to be depleted (less than expected) in arid regions and inflated (greater than expected) in wet regions. However, national-scale generalizations about streamflow modification and land use can be obscured by different land and water management within individual watersheds (local scale).

Summertime stream water temperatures were modified throughout the Nation and in all types of land uses. Average summertime water temperature was either cooler or warmer than natural at 17 percent of assessed streams. A major cause of modified stream temperatures is the loss of shading from riparian trees. Cooling of stream water temperatures can also result from artificial inputs of ground water, imported water from other river basins, or from the release of waters from the bottom of large reservoirs.

Removal of stream-side trees and other natural vegetation by agriculture and urban development is pervasive but was particularly severe in heavily agricultural areas such as the Midwest and western basins, and in urban areas such as the Atlantic coast.

Elevated salinity levels in streams and rivers occur throughout the Nation in basins with substantial urban and agricultural land use. Elevated salinity in urban settings is most prevalent in the northern states that receive relatively high snowfall, which suggests that road de-icing is a significant salt source. Other sources of salinity in urban streams include wastewater effluent and aged septic systems. The largest sources of excess salinity in agricultural streams include fertilizer applications and irrigation waste water.

Nutrient concentrations in stream water are up to six times greater than background levels in urban and agricultural lands across the Nation according to a national assessment of nutrient concentrations in streams from 1992 through 2004 ( Dubrovsky and others, 2010). Total nitrogen concentrations generally were highest in streams within agricultural areas of the Midwest, Northwest, and Northeast, where the highest nitrogen applications occur. Total nitrogen concentrations in urban areas were typically at intermediate levels.

One or more pesticides exceeded water-quality benchmarks in more than half of the streams assessed according to a comprehensive national assessment of pesticide concentrations in streams from 1992 through 2001 (Gilliom and others, 2006). Pesticide concentrations exceeded one or more benchmarks at 83 percent of urban sites and 57 percent of agricultural sites. The pesticides contributing to the potential toxicity of mixtures vary geographically according to their use across the Nation. Patterns in the relative contribution of different pesticides to the potential toxicity of mixtures reflect the geographic distribution of crop types among agricultural settings. Insecticides were the dominant pesticides contributing to potential toxicity. Diazinon was the dominant insecticide contributing to potential toxicity in urban settings during the study period.

A national assessment of the occurrence and distribution of contaminants in stream bed sediments reported that aquatic-life benchmarks for pesticide compounds were exceeded at 70 percent of assessed streams in urban settings and 30 percent of streams in agricultural settings (Gilliom and others, 2006). The potential toxicity of contaminant mixtures in stream sediments was also higher in urban than in agricultural streams. Mixtures most likely to be toxic occurred in 31 percent of urban streams, compared to just 4 percent of agricultural streams. Sediment contaminant mixtures in agricultural sites often include legacy organochlorine insecticides such as DDE, which is a breakdown product of DDT. More generally, sediment contaminant mixtures in urban streams are often dominated by polycyclic aromatic hydrocarbons (PAHs).


Biological Condition Assessment

How was biological condition determined?

The NAWQA Program used a consistent approach for assessing biological condition of algae, macroinvertebrate, and fish communities across the diverse landscapes of the Nation. Biological condition was assessed by comparing observed (O) community attributes (such as number of native species) to those expected (E) if the community was minimally disturbed by human activities. The observed attribute (O) is derived from a sample collected at the stream site being assessed, whereas the expected (E) condition is estimated from data collected at a set of environmentally similar reference sites. Because variation in environmental settings is accounted for in this approach, departures of O from E are likely the result of human-caused changes to the stream environment. Further, because O/E is standardized to each stream’s natural potential (that is, expressed as a percentage of the expected condition), data can be aggregated and interpreted across diverse geographic regions.

How were biological communities classified as “altered” or “unaltered”?

Each biological community was classified as “altered” if its O/E value was less than that of 90 percent of the reference sites within its respective region; otherwise, sites were classified as “unaltered”. For the integrated assessment, a stream was considered biologically altered if any one community was altered. This approach assumes that each of the three communities has equal ecological importance, which is reasonable given the major roles of algae, macroinvertebrate, and fish communities in streams. Importantly, this simple classification of biological condition is based on statistical properties unique to the data in this study and therefore not related to criteria used by states and other monitoring jurisdictions to assess beneficial use attainment.

How was reference condition characterized for a site?

Biological data from NAWQA, U.S. Environmental Protection Agency, and select state agencies were combined to characterize reference conditions. Reference sites were identified from this large set of sites by evaluating watershed and riparian land-cover disturbance, site-specific measures of habitat and chemical conditions, and professional judgment (Herlihy and others, 2008) . Separate reference sites were identified and used for each biological community. Nationwide, algal, macroinvertebrate, and fish communities were assessed using 276, 585, and 1,238 reference sites, respectively. Differences in numbers of reference sites among biological communities are largely due to data availability. A national database of reference sites was compiled by NAWQA and collaborators and is available at:

What were the main findings of the Biological Condition Assessment?

At least one biological community--algae, macroinvertebrates, or fish--was altered in 83 percent of the 585 assessed streams. In urban settings, 89 percent of assessed sites had at least one altered biological community, compared with 79 percent of sites in agricultural settings and 83 percent of sites in mixed-use lands. All three biological communities were altered in 22 percent of assessed streams.

Stream assessments based on a single community may underestimate the scope of altered biological communities due to human activities.

Streams with relatively intact biological communities can occur in watersheds with substantial amounts of agricultural, urban, and mixed land use. Streams with unaltered biological communities were present in 11–21 percent of assessed streams in all land-use settings.

Different combinations of agricultural practices, land features, and climate can lead to varying levels of altered biological communities. For example, altered biological communites was most severe in agricultural streams in intensively irrigated basins, such as the Central Valley, California, where chemical use and streamflow alteration can be pervasive. Biological communities in heavily cultivated basins in the corn belt, such as the Upper Mississippi, were relatively less severely altered, but are often influenced by near-stream cultivation practices and runoff laden with sediment and agricultural chemicals. Biological communities in agricultural areas dominated by pasture, as in the Ozarks, were altered less frequently than streams in other agricultural areas.

Different combinations of urban land use practices, land features, and climate can lead to varying levels of altered biological communities. Altered algae, macroinvertebrate, and fish communities were generally severe in most urban areas across the Nation, but local factors that influenced biological condition varied considerably among metropolitan areas. For example, some of the most frequently altered biological communities were in streams in the arid greater Los Angeles area, where treated wastewater effluent is often the dominant source of stream water, and many streams are channelized or concrete-lined. Frequency of altered biological communities was also high in streams of the Chicago suburbs, where dense urbanization occurred on lands already altered by intensive historic cultivation. Altered biological communities in streams of the Boston suburbs were associated with development of riparian zones and streamflow modification caused by mill dams. Comparatively better biological condition was observed in streams of the Atlanta suburbs, where stream channels were often within forested riparian zones and natural instream habitats were relatively intact.

How often were introduced species encountered at NAWQA sampling sites?

Introduced fish species were common, but most frequently encountered in the western United States. At least one species of introduced fish was collected at 50% of NAWQA sampling sites. Introduced fish species as a percent of total species richness was highest in streams in the western U.S., where native fish species richness is relatively low (Meador and others, 2003).

The Asian clam (Corbicula fluminea) was the most frequently observed introduced macroinvertebrate species encountered at 25 percent of NAWQA sampling sites. When present in large numbers, the Asian clam can foul power plant water intake pipes, industrial and municipal water systems, and irrigation canals.


Factors Associated with Diminished Biological Condition

What were the main findings of the assessment of factors associated with diminished Biological Conditions?

No single physical or chemical factor was universally associated with reduced stream health across the Nation. In basins within 6 metropolitan areas, reduced biological health in streams was associated with multiple physical and chemical factors.

The incidence of altered macroinvertebrate and fish communities increased in streams with greater depletion of annual high flows. The frequency of algal community alteration was not related to streamflow depletion.

The incidence of altered biological communities increased with greater amounts of agricultural or urban land development within stream riparian zones.

Biological communities, and particularly algae, were more frequently altered in streams with elevated nutrients relative to background levels.

Biological communities were more frequently altered in streams with increasingly elevated salinity relative to background levels.

Macroinvertebrate communities were more frequently altered in streams with higher potential toxicity of pesticide mixtures.

Macroinvertebrate communities were more frequently altered in streams with greater potential toxicity of sediment contaminant mixtures.


Implications of Findings of this Study

What are the implications of the findings of this study?

The presence of healthy streams in watersheds with substantial human influence indicates that it is possible to maintain and restore healthy stream ecosystems. Such streams can also offer insights into how stream health can be maintained amid anticipated changes in land use or restored when stream health has deteriorated as a result of human actions.

Assessments that are limited to a single biological community are likely to underestimate the effects of land and water use on stream health. Assessments of multiple biological communities increase our ability to detect streams with diminished health and provide a more complete understanding of how land and water use influence 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. Assessments and restoration efforts should therefore take a multifactor approach, wherein a number of factors—and their possible interactions—are considered. Understanding how these multiple factors influence biological communities is essential in developing effective management strategies aimed at restoring stream health.


Priorities for Filling Information Gaps

What are some of the most important steps needed to fill information gaps?

Reference Sites: Improve understanding of natural variability in physical, chemical, and biological characteristics at streams under minimal human influences. The ability to quantify man-made modification requires an understanding of the natural variability in physical, chemical and biological characteristics of streams. An expanded network of reference sites, particularly in regions that have widespread landscape modification, will be necessary to improve understanding of natural variability.

Predicting Baseline Conditions: Synthesize existing state and federal monitoring data to develop models that predict expected baseline conditions of key physical and chemical factors in streams, such as salinity, sediment, and water temperature. Greater use of the water-quality data portal would increase access to state and federal monitoring data and enhance the ability to synthesize large amounts of data for model development.

Understanding Multiple Factors: Improve assessment and understanding of the effects of the interactions of multiple man-made factors on biological communities. A major challenge to understanding why biological communities are altered is the ability to unravel the effects of many interacting natural and man-made factors. New studies are needed to specifically assess the interactions of multiple factors on stream health.

Tools for Decision Making: Improve the availability of tools useful for decision making. Increased understanding of the ways in which land and water management modify key physical and chemical characteristics of streams--and in turn influence stream health--should be accompanied by decision-support tools that allow predictions of the effects of alternative management actions.

Long-term Monitoring: Sustain and expand long-term monitoring of biological, chemical, hydrological, and other ecological characteristics for trends. Long-term, consistent data for assessing trends is essential for tracking biological responses to management practices as well as natural and human- influenced variation in climate.


Supporting Information for this Study

Whom can I contact for more information?

Daren M. Carlisle (Email: phone: 703-648-6890)

Where can I get more information on NAWQA biological assessment tools?

Field Sampling:

Revised methods for characterizing stream habitat in the National Water-Quality Assessment program (USGS Water-Resources Investigations Report 98-4052)

Revised protocols for sampling algal, invertebrate, and fish communities as part of the National Water-Quality Assessment Program (U.S. Geological Survey Open-File Report 02-150)

Taxonomic Quality Assurance and Sample Processing:

Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program (U.S. Geological Survey Water-Resources Investigations Report 98-4239)

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory-- Processing, taxonomy, and quality control of benthic macroinvertebrate samples (U.S. Geological Survey Open-File Report 00-212)

Protocols for the analysis of algal samples collected as part of the U.S. Geological Survey National Water-Quality Assessment Program (Patrick Center for Environmental Research, Report No. 02-06)

Diatoms of the United States: Tool for Taxonomic Consistency

A National Database of Aquatic Bioassessment Data:

BioData Retrieval System

Data Processing Tools to Facilitate Analysis and Interpretation

Invertebrate Data Analyses System (IDAS)

Algal Attributes: An Autecological Classification of Algal Taxa Collected by the National Water-Quality Assessment Program

Invertebrate and Fish Traits and Tolerance Data

National Repository of Reference-Site Data for Rivers and Streams

More Information on NAWQA and other Studies

Focused Biological Assessments in Urban and Agricultural Settings

Effects of Urbanization on Stream Ecosystems: USGS Circular 2012–1373

Effects of Nutrient Enrichment in streams in Agricultural Basins


Where can I learn more about all NAWQA studies?

NAWQA Program homepage:


Where can I get related information?

EPA National Surveys of Aquatic Life:

U.S. Environmental Protection Agency’s Wadeable Streams Assessment

U.S. Environmental Protection Agency’s National Aquatic Resource Surveys


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