California Water Science Center

Aquatic Ecology : Cycle I Activities (1994 - 2004)
Aquatic Ecology: Study Design

Ecological Studies are an integral part of the approach used by NAWQA to assess water quality. Information on biological communities and habitat characteristics contributes to the conceptual model of factors that affect water quality and to improved understanding of the relation among physical, chemical, and biological characteristics of streams. Fixed-Reach Assessments and Intensive Ecological Assessments provide an initial evaluation of the linkages among physical, chemical, and biological conditions within the Study Unit. Ecological Synoptic Studies provide a much more complete geographic representation within the Study Unit, but for a more limited set of physical, chemical, and biological characteristics.


Major ecological regions of the Sacramento River Basin.  Map is taken from Omernick, J.M. 
		(1987) Aquatic ecoregions of the conterminous United States.

Three taxonomic groups--fish, invertebrates, and algae--are sampled because they respond differently to various environmental stresses. Fish are valuable biological indicators of long-term water-resource conditions because they are long lived (years to decades) and have considerable economic value and public interest. Benthic invertebrates (aquatic insects, mollusks, crustaceans, worms) have life cycles (from months to a few years) that are intermediate between fish and algae, have close association with streambed sediments, and can be used for characterizing changes in water quality over small spatial area. Algae respond quickly (within days to weeks) to changes in their environment and serve as valuable biological indicators of rapid changes in water-resource conditions.

Gilliom, R.J., Alley, W.M., and Gurtz, M.E., 1995, Design of the National Water-Quality Assessment Program--Occurrence and distribution of water-quality conditions: U.S. Geological Survey Circular 1112, 33 p.
Occurrence and Spatial Distribution Surveys for Bed Sediment and Tissue

Two types of surveys are completed in NAWQA investigations to obtain information on the occurrence and distribution of hydrophobic organic contaminants and trace metals and other elements in streambed sediment and tissues of aquatic organisms. The Occurrence Survey is designed to provide information throughout the study unit. Sites are chosen on the major rivers and on smaller streams which may be important because of land uses (transport of pesticides or other organic contaminants, or metals) or because of distinctive geological features (geological deposits of specific trace metals, for example). Interpretation of data from the Occurrence Survey leads to the design of a Spatial Distribution Survey. A Spatial Distribution Survey is designed to provide more information on the distribution of specific contaminants within a study unit. The Spatial Distribution Survey for the Sacramento River Basin study was focused on trace elements, specifically mercury.

Seventeen sites were sampled for the Occurrence Survey and 19 were sampled for the Spatial Distribution Survey.

Data collected:

Occurrence Survey
Spatial Distribution Survey for Metals in Streambed Sediment


Ecological Studies: Fixed Reach Assessment

Ecological studies combine descriptions of fish, benthic invertebrate and algal communities, and habitats with physical and chemical data to provide an integrated assessment of water quality within selected environmental settings. These studies are used to assess trends in water quality, and investigate the influence of major natural and human factors on water quality.(Gilliom, 1995)

Data Collected:
Algae, benthic invertebrates, and fish were collected, and instream and riparian habitats were described at 13 sites from 1996 - 1998.


Ecological Studies: Intensive Ecological Assessment

The Intensive Ecological Assessment was done to provide information on spatial and temporal variability of biological communities and habitat characteristics. Spatial variability was addressed by sampling three similar reaches at two stream sites (Multi-Reach Assessment). Temporal variability was addressed by sampling one reach at each site annually during the three-year intensive data collection period (1996, 1997, 1998) (Single-Reach, Multi-Year Assessment).

Three types of algae and invertebrate samples were collected:

  • The richest targeted habitat samples were collected from the habitat expected to yield the greatest diversity of organisms and therefore expected to be the most sensitive to change because potential changes are the largest. Relative abundance data were obtained.
  • The depositional targeted habitat samples were collected where fine grained sediments are most abundant. These samples were expected to be sensitive to contaminants adsorbed to sediment particles because it samples organisms most closely associated with that habitat. Relative abundance data were obtained.
  • The qualitative multi-habitat samples were collected from all habitat types present to establish species richness. These samples were expected to be sensitive to loss of sensitive species that might be missed by the more specific samples. Only presence/absence data were obtained. A single fish sample was taken, providing data on relative abundance of species at the site.
Data Collected:
Ecological Studies: Community Assessment Synoptic

Ecological Synoptic Studies are short-term investigations of specific ecological characteristics within all or part of a Study Unit. Their roles in the NAWQA study design are to provide improved spatial resolution compared with fixed-site sampling and to evaluate the spatial distribution of selected ecological characteristics in relation to causative factors, such as land uses, contaminant sources, or instream habitat conditions. Ecological Synoptic Studies supplement information from the more comprehensive data collected at Basic and Intensive Fixed Sites by targeting specific and more narrowly defined conditions for ecological characterization at more locations.

The primary focus of sampling activities was to document water-quality conditions at lower elevations where human disturbances are prevalent. The secondary purpose was to document gradients in macroinvertebrate assemblages and environmental conditions from the valley floor to higher elevations in the Sierra Nevada. All sites were sampled at least once during low-flow conditions during the late summer or early autumn. Twenty-three sites were sampled.

Map showing ecological sites in the Sacramento valley

Factors affecting communities in the study unit

One major factor that has affected aquatic communities in the Sacramento River Basin is habitat modification. The Sacramento River and most of its tributaries are modified by dams or diversions. Habitat modifications affect the temperature, nutrient load, and riparian and in-stream habitat in the Sacramento River Basin to the extent that it affects the aquatic communities. Temperature alterations can cause direct stress to aquatic organisms or provide an environment only suitable for the more tolerant introduced species. Another major factor that may be affecting aquatic communities in the smaller Sierran or coastal tributaries is off stream diversion of water for consumptive uses. Continuous runoff into these streams is needed to maintain native populations, biodiversity and provide habitat for spawning fish species. When water is diverted away from these streams the aquatic habitat and communities are affected.


Important Ecological Issues

The important ecological issues for the Sacramento River Basin are centered around meeting the requirements of the Endangered Species Act, the Central Valley Improvement Act, and the preservation of biodiversity in aquatic communities. There are less direct aquatic issues that may impact habitat such as maintaining wetlands and rice stubble habitat for waterfowl. These issues all involve the availability and quality of water in the basin.

The National Marine Fisheries Service and Fish and Wildlife Service are required to preserve populations of the endangered winter run Chinook Salmon as well as the spring run, which is a species of special concern. The Delta Smelt is a threatened species in the Sacramento and San Joaquin Delta that requires specific flows and water quality from the Sacramento and San Joaquin Rivers to maintain their population. The Central Valley Improvement Act federally mandates that restoration for four races of Chinook salmon, steelhead, stripped bass, American shad, and white and green sturgeon to levels at least twice the mean estimated natural production for the baseline period (1967-1991) in the San Joaquin and Sacramento Rivers. To reach these goals minimum water quality and habitat conditions must be maintained by state and federal agencies. Providing for biodiversity in aquatic systems is an overall goal of several public and private agencies. There are local government and private community groups that are very concerned with water quality along the Sacramento River and its tributaries. The city and county of Sacramento as well as other public agencies and private community groups do intermittent monitoring of water quality, but there has been no long term water quality or ecological studies in the Sacramento River basin. The agencies and communities within the basin have been very supportive of the proposed NAWQA monitoring.

Picture showing Spring Creek and Keswick Dam

Contaminant issues affecting water quality and aquatic communities in the Sacramento Basin are acid mine drainage, agricultural runoff, sources of dioxin from a paper mill, mercury inputs, and municipal non-point source pollution. Acid mine drainage from Iron Mountain Mine in the northern part of the study unit introduces metal contaminants during high flow events into the Sacramento River. Just downstream of this site is the spawning area for the endangered winter run Chinook Salmon. Mercury is a contaminant of particular concern, particularly in the lower Sacramento River. The sources of mercury include abandoned mines and geological sources in the Coast Ranges, runoff from abandoned gold mines in the Sierra Nevada, and atmospheric sources. Mercury contamination of fish is a problem in the lower Sacramento River and in the San Francisco Bay. The California State Toxic Substance Monitoring Program showed elevated levels of mercury in samples taken from the American River, Feather River, Yuba River and Cache Creek. Runoff from orchards, rice fields, pasture and other crops have been known to contribute agricultural chemicals to the Sacramento River and its tributaries, providing a source of contaminants to the aquatic ecosystem. Elevated levels of dioxin had been detected downstream from a pulp and paper mill. The source of this contaminant has been stopped but dioxin may still be persistent in the environment. There are several inputs of effluent from treatment plants and municipal sources up and down the Sacramento River.


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