# 

# Water-Quality and Biological Conditions in the Lower Boise River, Ada andCanyon 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 EnvironmentalQuality

 

This report is also available as a pdf.

 

## Abstract

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  concentrationsover 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 thosein 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 degradedwater 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 lowestRFI score was at Parma, near the mouth of the river.

## Contents

ABSTRACT

INTRODUCTION

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

SelectedPrevious Investigations

StudyBackground

Purpose  and Scope

Acknowledgments

DESCRIPTIONOF THE LOWER BOISE BASIN

DATACOLLECTION AND ANALYSIS

SurfaceWater

Biological

SamplingFrequency

Quality  Control Samples

HYDROLOGICCONDITIONS

SurfaceWater

Ground  Water

WATER-QUALITYCONDITIONS

GeneralWater Properties

Suspended  Sediment

SuspendedSediment Concentrations

Seasonaland Long-Term Trends in Suspended Sediment Concentrations

Suspended  Sediment Loads

Nitrogen

NitrogenConcentrations

Seasonaland Long-Term Trends in Nitrogen Concentrations

Nitrogen  Loads

Phosphorus

PhosphorusConcentrations

Seasonaland Long-Term Trends in Phosphorus Concentrations

Phosphorus  Loads

Indicatorsof 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

BIOLOGICAL CONDITIONS

Benthic  Macroinvertebrate Metrics and Indices

Fish    Communities

Fish      Sampling Sites

Idaho        River Fish Index

SUMMARY          AND CONCLUSIONS

REFERENCES            CITED

APPENDIX:              Reconnaissance of Ground- and Surface-Water Interactions 

Introduction

Study Design and Sample Collection Methods

Results  of Ground- and Surface-Water Interactions

Conclusions

----

For sale by 

 

U.S. Geological Survey, 

Information Services  Box 25286, Denver Federal CenterDenver, CO 80225

 

For more information about the USGS and its products:  Telephone: 1-888-ASK-USGS

World Wide Web: http://www.usgs.gov/

 

 

Any use of trade, product,  or firm names in this publication is for descriptive purposes only and does  not imply endorsement  by the U.S. Government.Although this report is in the public domain, permission  must be secured from the individual copyright owners to reproduce any copyrightedmaterials contained within this report.

 

 

----

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 InvestigationsReport 2004–5128, 80 p.

 

This  report is available online in Portable Document Format (PDF). If you do not have  the **Adobe  Acrobat PDF Reader**, it is available for free download from Adobe Systems  Incorporated.

 

Download the text of the report (PDF, 3 MB)

Download the cover of the report (PDF, 1.8 MB)

 

DocumentAccessibility: Adobe Systems Incorporated has information about PDFs and thevisually impaired. This information provides tools to help make PDF filesaccessible. These tools convert Adobe PDF documents into HTML or ASCII text,which then can be read by a number of common screen-reading programs thatsynthesize text as audible speech. In addition, an accessible version of AcrobatReader 5.0 for Windows (English only), which contains support for screenreaders, is available. These tools and the accessible reader may be obtainedfree from Adobe at **AdobeAccess**.

 

For more information about USGS activities in Idaho, visit  the **USGS  Idaho District home page**.

 

 

Top

----