USGS
Water Resources of Idaho

National Water-Quality Assessment (NAWQA) Program
Upper Snake River Basin Study

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Reprinted with permission from Idaho Wildlife Fall 1995, volume 15, issue 5.
A publication of the Idaho Department of Fish and Game. blueshade line

Drawing A "Big Picture" of Idaho Waters

By Terry Maret and Walton Low¹


Two truths are self-evident when it comes to the relationship between rivers and people: Rivers reflect the human stewardship of the land bordering them, and rivers convey human waste. Over time, therefore, human activities can disrupt a river's natural balance and cause unpredictable and long-term effects on its biological health.

Large rivers are particularly susceptible to cumulative effects of pollution, but many large rivers have not been well studied because of their size and complexity. An example is the reach of the Snake River in Idaho between Milner Dam and King Hill, called the Middle Snake, which is showing the effects of excess nutrients (nitrates and phosphorus), heavy sediment load and flow manipulation--all results of human activities. To remedy this lack of knowledge so these problems can be addressed, scientists from several agencies are studying the river. One of the most promising studies is the National Water-Quality Assessment (NAWQA) Program, which is collecting data on the Middle Snake and the entire upper Snake River Basin of Idaho and western Wyoming.

NAWQA (pronounced "na-qua") is a program of the U.S. Geological Survey, the federal agency known best for producing the useful topographical maps people take on their hunting or fishing trips (USGS-More Than A Mapmaker, 35 Kb). NAWQA field teams of study-unit scientists consist of surface-water and ground-water hydrologists, geographers, biologists, and technicians. Their findings are integrated into a comprehensive report card of water resource health. In 1991, NAWQA programs began in 20 of the nation's large river basins.

The NAWQA study schedule calls for four to five years of intensive assessment followed by five years of low-intensity assessment; then the cycle repeats(NAWQA Plan of Action, 202 Kb). To help ensure the information collected is relevant to local and regional interests, each study unit team meets regularly with a liaison committee representing other federal, state and local agencies, universities and the public.

The upper Snake River Basin study-unit team is based in Boise. Field office teams in Twin Falls and Idaho Falls help collect data. Given the basins's size (about 36,000 square miles containing almost 8,500 stream miles) and geographic diversity (desert to alpine mountain meadows), this assessment is no small undertaking. However, data analysis and interpretations are made easier by using a computerized Geographic Information System (GIS). GIS uses satellite data to distinguish various land uses over large areas so relationships between land uses and water quality can be determined.

The Snake River--A Living System

A river is more than just flowing water. A river lives, dynamic in energy and movement, teaming with organisms. These life forms are essential to the river's well-being. Certain physical and chemical qualities must be present before a river will thrive, supporting a food chain or web that includes everything from the smallest algae to the largest fish. Partners to a river system are land, which furnishes basic nutrients, and sunlight, which provides energy.

Life in any natural aquatic system is controlled by biotic (living) and abiotic (nonliving) factors. Biotic factors operate by predation and competition for food and living space. These factors existed long before humans and are extremely important in maintaining natural balance and stability. One biotic factor that can be influenced by human activities is the introduction of non-native species. When that happens, native species often lose living space, compete unsuccessfully for food or become prey. This has happened recently in the Middle Snake River and some of its major tributaries. Native, cold-water snail species have markedly decreased (some are federally listed as threatened or endangered) while more pollution-tolerant, introduced species such as the New Zealand mudsnail have increased.

Abiotic factors are environmental conditions for which every organism has specific requirements or tolerances. Some of the more important include water quality (nutrient and sediment concentrations), water quantity, temperature and habitat. Salinity, for example, is an abiotic factor that influences the distribution of fishes throughout the world. Natural or human barriers are particularly important abiotic factors in the upper Snake River Basin. Shoshone Falls near Twin Falls is a natural barrier to fish passage. It once marked the historical upstream limit of anadromous (ocean-migrating) Snake River salmon and steelhead trout. Today, hydropower dams stop fish from migrating up the Middle Snake River and its tributaries at Hells Canyon, some 360 river miles downstream from Shoshone Falls.

Measuring Stream Life

Aquatic biological assessments are an integral part of NAWQA for a number of reasons. First and foremost, assessing stream communities tells us how safe the water is for recreation, such as swimming or fishing, or whether it's safe to eat the fish we catch. Assessments also describe the stream's quality for fish and wildlife propagation. In addition, monitoring aquatic communities measures species diversity and can help describe long-term trends in river health.

Because most upper Snake River Basin streams historically have supported predominantly cold-water aquatic life (species adapted to water temperatures below 70 F), reductions in these organism types indicate changes in the river's health. The Middle Snake River, which once supported a cold-water trout fishery, now for the most part sustains pollution-tolerant warm-water and nongame fish species such as suckers and carp. The relationship of trout to nongame fish varies at different sites in the upper Snake River Basin, however. These variations correspond to the degree of human disturbance, from minimal to heavy, to which their habitat has been subjected.

NAWQA scientists follow published national procedures, which add consistency to the program. Before the NAWQA monitoring network was designed, scientists summarized existing data on aquatic biology and contaminants in biological tissue into a technical report. This step ensured that data gaps were identified and important environmental issues were considered in the sample design. Biological data collected from rivers in the basin include contaminants in fish and other aquatic organisms; characteristics of fish, benthic (bottom-dwelling) invertebrates, and algal communities; and measurements of instream and riparian habitat quality.

Checking for Contaminants in Biological Tissue

Researchers analyze biological tissues for a wide variety of chemical contaminants: trace metals such as lead, mercury and zinc; organochlorine pesticides such as DDT, dieldrin and chlordane; and PCB's, a mixture of compounds primarily used in electric capacitors and transformers. They analyze whole fish (suckers and carp, for example) for organic compounds, and analyze aquatic insects (caddisflies) and fish livers for metals. This information will reveal more about when and where contaminants occur in the environment and whether the levels measured could potentially affect humans or wildlife. To ensure that fish are safe for human consumption, follow-up sampling could include analyzing game-fish tissue for the contaminants for which guidelines have been established.

Assessing Biological Communities

Biological communities reflect many chemical and physical conditions of the river and surrounding land. Therefore, surveying them is an essential component of any water-quality assessment. A river's fish, benthic invertebrates and algae directly mirror its health. Usually, a diverse community with many species indicates good water quality. Polluted waters, on the other hand, generally have fewer species, many of which can tolerate pollution and procreate rapidly.

However, preliminary results show this is not necessarily true of fish communities in Idaho's cold-water streams. Here, high-quality waters at higher elevations usually hold fewer fish species than do downstream waters. This is because cold-water streams generally do not offer the food chain and temperature that many fish species prefer. In addition, as stream size increases, more habitat types are available for native and introduced species to use (see chart, 134 Kb).

The first step in assessment is to characterize the biological conditions we would expect to see in minimally disturbed streams, such as the number and kinds of species likely to be in different-sized rivers at various elevations. These are benchmarks against which to measure sites that may be affected by various land uses. Benchmark conditions give resource managers some idea of how severe a water-quality problem is and realistic goals to strive for in resource recovery and conservation activities.

NAWQA researchers sample fish communities primarily by electrofishing. After stunning the fish, they identify all species, take body measurements and note fish showing signs of disease or external abnormalities (frequent occurrences of diseased fish has been linked to polluted waters).

The researchers determine whether the trout they collect are of hatchery or wild origin. Added to the body-length data, this fact helps them estimate that water's natural trout reproduction, an important use of Idaho rivers. Knowing how many trout a stream produces tells a lot about the quality of its water and spawning habitat. The researchers also compare numbers of introduced species to native species. Cold-water rivers degraded by pollution often have fish communities made up of more pollution-tolerant introduced species like carp and sunfish.

Bottom-dwelling invertebrates (aquatic insects, clams, snails, crayfish and worms) are important indicators of water quality because they are sensitive to the presence of contaminants in the water and sediments. Also, unlike fish, which are highly mobile and often can avoid contaminated areas, invertebrates are less able to escape exposure to contaminants. Many invertebrates found in riffles are also sensitive to excessive fine sediment and will soon disappear if their living space is covered with silt or sand. This makes them excellent indicators of excessive sediment, which has been identified as the number one pollutant in Idaho's surface waters.

Aquatic invertebrates, especially aquatic insects, are the food many species of fish prefer. Consequently, the kinds and numbers of invertebrates found in a river can be directly related to the occurrence of certain fish species.

Algae, groups of tiny aquatic plants, are often overlooked, but they are very important to stream health. They are the beginning of the complex food chain that supplies food for higher life forms. Rivers typically contain hundreds of algal species and many indicate by their presence specific water-quality conditions. Excess nutrients such as nitrogen and phosphorus originating from chemical fertilizers or animal wastes usually will increase the amount of nuisance algal growth. The resultant dense mats of algae can choke off waterways to boaters and, through decay and respiration, can reduce oxygen to levels lethal to fish and other aquatic organisms.

NAWQA scientists also identify the various algal species and check how much growth is occurring on the stream bottom. The amount of stream shading by streamside trees and brush can affect the amount of algal growth. Heavily shaded streams exhibit less algal growth than streams open to full sunlight. With shade, cold-water desert streams may remain cool enough in summer to support trout.

Examining River Habitat

"Habitat" is all the factors that describe the stream environment and its relationship to aquatic organisms, which largely depend on the quality and quantity of the chemical and physical properties of their environment. Water-quality characteristics like turbidity, dissolved oxygen, water temperature and nutrients determine the abundance and diversity of aquatic life. Measuring streambed material, cover and shoreline features discloses the available living space for aquatic organisms. Trout, for example, require large amounts of clean gravel to spawn. They also need cover such as woody debris and undercut banks for protection from predators. Measuring bank characteristics such as shade from riparian vegetation (plants growing on land immediately adjacent to streams) further defines habitat quality.

Habitat sampling is based on a multiple-scale design incorporating information at basin, stream segment and stream reach levels. Basin-level or watershed characteristics are obtained from GIS databases on hydrology, geology, soils, land use and vegetation. Stream segments are defined by their tributary junctions or major discontinuities, such as waterfalls or other landforms. Segment-level data include stream meandering, gradient, elevation, dams, diversions and other water management features. A stream reach consists of a section of the stream segment one-eighth to one-fourth mile long where the NAWQA team collects fish, invertebrates, algae and information on habitat conditions.

Researchers measure habitat at cross-section transect points along the stream to learn water depth and velocity, channel width, flow amount, substrate composition and habitat cover types. They take photographs to document existing conditions and changes over time and to assess vegetation types and abundance within the riparian area to determine dominant plant species and erosion potential.

Putting the Puzzle Together

NAWQA is designed to integrate chemical, physical and biological characteristics of the nation's surface and ground water and link them with land use. As these fundamentals become known, decision-makers will be able to generate policies and management actions to improve water quality in Idaho and throughout the nation. All the NAWQA data will be stored in a National Water Information System, which will provide for easy public access. Descriptive and interpretive reports covering individual study units as well as regional and national assessments will be prepared. The NAWQA Program will provide citizens with the "big picture" using multiple lines of evidence to evaluate complex and diverse hydrologic systems.

Once the first cycle of this program is completed, landowners, scientists, politicians, sportsmen and everyone else will have a much clearer picture of the health of the upper Snake River and all the factors affecting one of Idaho's most important waterways.


Walton Low and Terry Maret are project chief and study-unit biologist, respectively, for the upper Snake River Basin NAWQA Program.

¹U.S. Geological Survey, 230 Collins Rd. Boise, Idaho 83702-4520

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