Scientific Investigations Report 2006-5111

Scientific Investigations Report 2006-5111

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Within the last century, the lower Boise River downstream of Lucky Peak Dam in southwestern Idaho has been transformed from a meandering, braided, gravel-bed river that supported large runs of salmon to a channelized, regulated, urban river that provides flood control and irrigation water to more than 1,200 square miles of land. In some places, the river is one-half the width it was before it was dammed. The lower Boise River fish communities are impacted by flow alterations, habitat loss, and poor water quality. As water demand increases for urban, domestic, and agricultural uses, so does the impact on the fish communities. The river’s flow is regulated by upstream dams and downstream irrigation returns. In fact, the current flow in the lower Boise River is opposite to that of pre-dam era, with lower flows in the winter and higher flows in the summer. The lack of higher flows to recruit and move gravel for riffle habitat and to mobilize fine sediment has caused embeddedness throughout the river that measures between 50 and 75 percent. The quality of water decreases in a downstream direction with increasing temperatures and nutrient and sediment concentrations. Although rainbow trout are stocked at a rate of 56,000 fish per year in the lower Boise River, the lack of colder temperatures downstream has reduced natural spawning of this species.

Fish data from the U.S. Geological Survey (USGS) and Idaho Department of Fish and Game (IDFG) collected since 1974 were combined to report the status of fish communities in the lower Boise River. Twenty-two species representing 7 families of fish have been identified in the lower Boise River: 3 salmonids (trout and whitefish), 2 cottids (sculpins), 3 catostomids (suckers), 7 cyprinids (minnows), 4 centrarchids (sunfish), 2 ictalurids (catfish), and one cobitidae (loach). Of these, 13 are native species, 5 are cold water species, 9 are cool water species, and 8 are warm water species. Most of the warm water species are found in the lower reaches of the river. Of the salmonid species, mountain whitefish have been found throughout the lower Boise River, and rainbow and brown trout have been found upstream of Eagle Road. Sculpin, a cold water, bottom-feeding fish, has been found only in the upstream reaches upstream of Glenwood Bridge. Suckers have been found throughout the river, and tolerant species such as carp, northern pikeminnow, bass, and catfish have been found primarily in the lower reaches. Index of Biotic Integrity (IBI) scores calculated for USGS and IDFG sampling events between 1988 and 2004 decreased in a downstream direction, with two of the lowest scores (indicating poor biotic integrity) measured at Middleton (40) and near the mouth (11), respectively. IBI scores for each sampling reach remained similar over time except for the reach downstream of the Lander WTF. The IBI scores for the reach downstream of the Lander WTF (reach 5) increased from a score of 36 in 1988, indicating poor biotic integrity, to 73 in 2003, indicating intermediate biotic integrity. The increase in IBI score at this site may be an indication of increased water quality and reflects the increased number of sculpin found in 2003. IBI scores for all sites were negatively correlated with maximum instantaneous water temperature, specific conductance, and suspended sediment; as well as the basin land-use metrics of area of developed land, impervious surface area, and number of major diversions within a subbasin. Fish communities downstream of Middleton consisted primarily of tolerant species and omnivorous feeders, whereas fish communities in the upstream most reach downstream of Barber Dam consist of only 2 percent tolerant species and were piscivores and invertivores.

Fish communities downstream of the Lander WTF generally had lower IBI scores, an increase in tolerant species, and a decrease in percentage of cold water species. Sculpin were not found downstream of Glenwood Bridge in the lower Boise River, possibly due to decreases in habitat and water quality. Length-weight relations for mountain whitefish, an indicator used to determine the condition of the species’ population in the lower Boise River, were similar to those found both in regional populations and in least-disturbed rivers in southern Idaho.

The fish communities in the lower Boise River have changed in response to changes in habitat, land use, and water quality. As the human population increases in the lower Boise River Basin, the demand for both high-quality water and recreation in and around the river will affect aquatic communities, especially fish communities. Frequent and comprehensive monitoring of the lower Boise River fish communities will help to identify impacts and to sustain this beneficial resource.

Land use in the lower Boise River Basin is changing rapidly from a rural/agricultural community to an urban/residential community, and these changes may affect the lower Boise River fish community. Future assessments of status or changes in fish community and health in the lower Boise River should focus on the distribution of benthic species such as sculpin and the direct assessment of fish health. A more comprehensive evaluation of fish health that includes both indicators of exposure and potential effects of endocrine-disrupting chemicals could provide important information about the effects of pollutants on fish populations in the lower Boise River.

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