Water-Quality and Biological Conditions in the Lower Boise River, Ada and Canyon Counties, Idaho, 1994-2002

Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2004-5128


By Dorene E. MacCoy


Prepared in cooperation with Idaho Department of Environmental Quality


This report is also available as a pdf.



The water quality and biotic integrity of the lower Boise River between Lucky Peak Dam and the river's mouth near Parma, Idaho, have been affected by agricultural land and water use, wastewater treatment facility discharge, urbanization, reservoir operations, and river channel alteration. The U.S. Geological Survey (USGS) and cooperators have studied water-quality and biological aspects of the lower Boise River in the past to address water-quality concerns and issues brought forth by the Clean Water Act of 1977. Past and present issues include preservation of beneficial uses of the river for fisheries, recreation, and irrigation; and maintenance of high-quality water for domestic and agricultural uses. Evaluation of the data collected from 1994 to 2002 by the USGS revealed increases in constituent concentrations in the lower Boise in a downstream direction. Median suspended sediment concentrations from Diversion Dam (downstream from Lucky Peak Dam) to Parma increased more than 11 times, nitrogen concentrations increased more than 8 times, phosphorus concentrations increased more than 7 times, and fecal coliform concentrations increased more than 400 times. Chlorophyll-a concentrations, used as an indicator of nutrient input and the potential for nuisance algal growth, also increased in a downstream direction; median concentrations were highest at the Middleton and Parma sites. There were no discernible temporal trends in nutrients, sediment, or bacteria concentrations over the 8-year study.

The State of Idaho’s temperature standards to protect coldwater biota and salmonid spawning were exceeded most frequently at Middleton and Parma. Suspended sediment concentrations exceeded criteria proposed by Idaho Department of Environmental Quality most frequently at Parma and at all but three tributaries. Total nitrogen concentrations at Glenwood, Middleton, and Parma exceeded national background levels; median flow-adjusted total nitrogen concentrations at Middleton and Parma were higher than those in undeveloped basins sampled nationwide by the USGS. Total phosphorus concentrations at Glenwood, Middleton, and Parma also exceeded those in undeveloped basins.

Macroinvertebrate and fish communities were used to evaluate the long-term integration of water-quality contaminants and loss of habitat in the lower Boise. Biological integrity of the macroinvertebrate population was assessed with the attributes (metrics) of Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness and metrics used in the Idaho River Macroinvertebrate Index (RMI): taxa richness; EPT richness; percent dominant taxon; percent Elmidae (riffle beetles); and percent predators. Average EPT was about 10, and RMI scores were frequently below 16, which indicated intermediate or poor water quality. The number of EPT taxa and RMI scores for the lower Boise were half those for least-impacted streams in Idaho. The fine sediment bioassessment index (FSBI) was used to evaluate macroinvertebrate sediment tolerance. The FSBI scores were lower than those for a site upstream in the Boise River Basin near Twin Springs, a site not impacted by urbanization and agriculture, which indicated that the lower Boise macroinvertebrate population may be impacted by fine sediment. Macroinvertebrate functional feeding groups and percent tolerant species, mainly at Middleton and Parma, were typical of those in areas of degraded water quality and habitat.

The biological integrity of the fish population was evaluated using the Idaho River Fish Index (RFI), which consists of the 10 metrics: number of coldwater native species, percent sculpin, percent coldwater species, percent sensitive native individuals, percent tolerant individuals, number of nonindigenous species, number of coldwater fish captured per minute of electrofishing, percent of fish with deformities (eroded fins, lesions, or tumors), number of trout age classes, and percent carp. RFI scores for lower Boise sites indicated a decrease in biotic integrity of fish in a downstream direction; the lowest RFI score was at Parma, near the mouth of the river.




Historical Alterations of Water Quality and Biological Integrity in the Lower Boise Basin

Selected Previous Investigations

Study Background

Purpose and Scope




Surface Water


Sampling Frequency

Quality Control Samples


Surface Water

Ground Water


General Water Properties

Suspended Sediment

Suspended Sediment Concentrations

Seasonal and Long-Term Trends in Suspended Sediment Concentrations

Suspended Sediment Loads


Nitrogen Concentrations

Seasonal and Long-Term Trends in Nitrogen Concentrations

Nitrogen Loads


Phosphorus Concentrations

Seasonal and Long-Term Trends in Phosphorus Concentrations

Phosphorus Loads

Indicators of and Probable Controls on Algae Growth

Water Properties and Concentrations of Constituents Compared with Criteria, State Standards, Local Recommendations, and Guidelines

Fecal Coliform and E. Coli Bacteria

Fecal Coliform Concentrations

Seasonal and Long-Term Trends in Fecal Coliform Concentrations

Fecal Coliform Loads

E. Coli Concentrations

Fecal Coliform and E. Coli Concentrations Compared with Criteria


Benthic Macroinvertebrate Metrics and Indices

Fish Communities

Fish Sampling Sites

Idaho River Fish Index



APPENDIX: Reconnaissance of Ground- and Surface-Water Interactions


Study Design and Sample Collection Methods

Results of Ground- and Surface-Water Interactions


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Suggested citation:


MacCoy, D.E., 2004, Water-Quality and Biological Conditions in the Lower Boise River, Ada and Canyon Counties, Idaho, 1994–2002: U.S. Geological Survey Scientific Investigations Report 2004–5128, 80 p.


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