Scientific Investigations Report 2006-5111

Scientific Investigations Report 2006-5111

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Purpose and Scope

Fish community sampling has been included in some water-quality studies in the lower Boise River from 1974 to 2004. These sampling events have not been summerized in one report until now. These studies differed somewhat in objectives, sampling protocols, and findings. The data, however, can be compiled and summarized for selected reaches of the lower Boise River to further the understanding of the fish community and associated environmental conditions. The purposes of this report are to describe the occurrence and distribution of fish species of the lower Boise River using data collected by IDFG and USGS from 1974 to 2003 to describe temporal trends in fish-community structure and fish condition, and to identify environmental factors affecting occurrence, distribution, and community trends. Historic land and channel features from the late 1800s were used to compare fish habitat prior to and following hydrologic modification of the lower Boise River Basin.

Description of Lower Boise River Basin

The 1,290 mi2 lower Boise River Basin is located in Ada and Canyon Counties in southwestern Idaho between Lucky Peak Dam (river mile 64) and the confluence of the Boise and Snake Rivers (river mile 395) (fig. 1). The basin contains the most industrialized and urbanized areas in Idaho. In 2000, the population in Ada and Canyon Counties was about 432,300 (U.S. Census Bureau, 2002), which is 33 percent of Idaho’s population. Population in 2000 increased more than 46 percent over the 1990 population in these two counties.

The lower Boise River Basin is in the northern part of the western Snake River Plain (fig. 1), and it lies in a broad, alluvium-filled basin with several step-like terraces, or benches, which are more pronounced and continuous on the south side of the river. The upper basin, upstream of Lucky Peak Dam, is mountainous and sparsely populated. Downstream of Lucky Peak Dam, the basin floor slopes northwestward at a gradient of about 10 ft/mi. The altitude of the basin near Lucky Peak Dam is about 2,800 ft above sea level; the altitude near the river mouth is about 2,200 ft (Thomas and Dion, 1974). In addition to the lower Boise River, several tributaries are interconnected by a complex irrigation system of canals, laterals, and drains. Climate in the lower Boise River Basin is characterized as semiarid; winters are cool and wet, and summers are warm and dry. Some years considered to have normal to high amounts of precipitation are 1995 to 1998, and 2000; and some years categorized as severe drought are 1999, 2001, and 2002. Thomas and Dion (1974), Mullins (1998), and the lower Boise subbasin assessment conducted by the Idaho Department of Environmental Quality (1999) provide more information on the geography, geology, and climate of the lower Boise River Basin.

Flow in the lower Boise River between Lucky Peak Dam and the mouth is controlled primarily by reservoir regulation, irrigation withdrawals and return flows, and seepage of shallow ground water (Thomas and Dion, 1974). The three reservoirs upstream in the upper Boise River Basin have a combined storage capacity of about 1 million acre-ft. These reservoirs are managed primarily for irrigation and flood control, and secondarily for recreation and power generation (Mullins, 1998). Some storage is assigned to salmonid flow augmentation in Lucky Peak Lake as required by the National Marine Fisheries Service (NMFS) 1995 Biological Opinion for the Snake River Basin (Bureau of Reclamation, accessed March 2002, at

Land use and land cover in 1994 within the lower Boise River Basin included urban activities (4 percent); irrigated agriculture, pasture, and other agriculture-related activities (47 percent); and rangeland, water, and unclassified land (49 percent) (Kramer and others, 1994). Crops in the basin consist of alfalfa hay and seed, corn and corn seed, wheat, potatoes, onions, sugar beets, barley, spearmint and peppermint, and dry edible beans (Koberg and Griswold, 2001). This land use contrasts with that in the upper Boise River Basin, which consists primarily of logging and recreation. Parts of the upper basin were heavily mined for gold during the late 1800s and early 1900s (Love and Benedict, 1940; Chandler and Chapman, 2001).

Land use in the lower Boise River Basin has undergone major changes since 1994; particularly conversions of large tracts of farmland to residential subdivisions and commercial facilities, and conversions of many residential areas in and near cities to businesses, shopping centers, and parking lots. These land-use changes typically cause a reduction in agricultural non-point runoff, and may increase urban stormwater runoff to the lower Boise River and its tributaries, depending on the development practices implemented. Under the Clean Water Act, numerous public and private entities in the lower Boise River Basin are required to seek non-point discharge and elimination system (NPDES) stormwater discharge permits. These permits require these entities to implement best management practices that reduce pollutant loads to the “maximum extent practicable” (Johanna Bell, City of Boise, written commun., April 17, 2006). U.S. Environmental Protection Agency (EPA) regulation guidance and requirements are available online at (accessed June 15, 2006). State of Idaho guidance is available online at (accessed June 16, 2006). Boise municipal regulations and guidance are available online at the Partners for Clean Water web site at (accessed June 16, 2006). The City of Boise stormwater program is implementing a plan to reduce the stormwater load of sediment (p. 61 of Lower Boise River total daily maximum load [TMDL] at; accessed June 15, 2006) and total phosphorus. The stormwater sediment load reduction is a result of the development of a sediment TMDL (Idaho Department of Environmental Quality, 1999). Development of a total phosphorus TMDL and a temperature assessment are currently being done for the lower Boise River (Robbin Finch, City of Boise, written commun., November 2005).

Historical Changes in the Fishery

The fishery of the lower Boise has changed over time partly in response to multiple human impacts caused by development of the study area. Settlers began to divert water from the lower Boise for irrigation in the late 1800s and early 1900s; irrigation return flows were an early source of water-quality and stream habitat degradation. Also at that time, extensive mining began in the upper basin, and numerous lumber mills were operated east of Boise to supply timber for development (Stacy, 1993; Simonds, 1997). Temporal changes due to natural factors (climate change) in the lower Boise are unknown.

Soon after development began, farmers recognized the need for flood control and storage of irrigation water, which led to the 1902 “Boise Project,” one of the earliest projects by the Bureau of Reclamation (Stacy, 1993; Simonds, 1997). By 1906, the New York Canal and several small irrigation projects had been built as part of the Boise Project. One of the Bureau of Reclamation’s (BOR) “big dams,” Arrowrock, was built in 1915 on the mainstem Boise River, about 17 mi upstream of the City of Boise. The U.S. Army Corps of Engineers (Corps) built Anderson Ranch Dam on the South Fork of the Boise River (the world’s highest earthfill dam at the time of its completion in 1950). Anderson Ranch Dam is the uppermost storage facility on the Boise system located 42 mi upstream of Arrowrock Dam. Anderson Ranch Dam and Powerplant is a multiple-purpose structure that provides benefits in irrigation, power, and flood and silt control (accessed April 17, 2006, at: In 1957, the Corps built the third and final large dam, Lucky Peak, less than 10 mi upstream of the City of Boise, in response to concerns about potential flooding and to the need for additional irrigation water (Stacy, 1993). The construction of these dams affected the lower Boise fishery by blocking fish passage, changing the thermal regime and flow patterns of the river, modifying sediment transport and substrate size, and altering water quality and channel shape.

Progressive urbanization around the City of Boise increased the need to treat wastewater prior to discharge to the lower Boise River. The construction of wastewater-treatment facilities (WTFs) downstream of Boise in the early 1950s helped to disinfect wastewater entering the river, but introduced toxic concentrations of chlorine that resulted in frequent fish kills (Stacy, 1993). In the late 1950s, the lower Boise River was identified as one of the three most polluted waters in Idaho (Casey and Webb, 1996; Chandler and Chapman, 2001). In 1976, a second outlet was proposed for installation in Lucky Peak Dam to implement a minimum flow of about 150 ft3/s during winter, which helped to dilute effluent. According to the IDEQ, minimum flow varied as a result of water allocations downstream (Idaho Department of Environmental Quality, 1999). Continuing cleanup efforts in the lower Boise River Basin include upgrading WTFs and implementing best management practices (BMPs) for urban and agricultural runoff.

Prior to construction of dams, levees, and extensive irrigation in the lower Boise River Basin, a large (as wide as 0.75 mi) hyporheic zone (an area beneath the main channel where surface water interacts with ground water) existed. The river’s interaction with the hyporheic zone allowed the river to develop side channels and other habitat for refuge and areas ideal for salmon spawning and rearing (David Blew, Idaho Department of Water Resources, oral commun., 2002). Operation of the three Boise River dams for irrigation and flood control created a flow regime with higher than natural flows during the peak irrigation season (April through September) and lower than natural flows during the nonirrigation season (October through March). The change in hydraulic regime and the construction of levees has caused the lower reaches of the lower Boise River to incise to the point that depositional areas, backwater sloughs, and wetlands associated with the hyporheic zone have diminished (David Blew, Idaho Department of Water Resources, oral commun. 2002; MacCoy and Blew, 2005). For further information on the effect of dams on alluvial rivers please refer to Williams and Wolman (1984), Collier and others (1996), and the World Commission on Dams (2000).

The lower Boise fishery was described in the early 1800s as the “most renowned fishing place in the country,” because of the large numbers of salmon caught there (Pratt and others, 2001). The lower reaches of the Snake and its adjoining tributaries, which include the lower Boise River, were highly productive fisheries in the early 1800s for the Shoshone‑Bannock Tribes (accessed March 2005, at The historical distributions of Chinook salmon (Onchorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) were evaluated by Idaho Power Company (IPC) as part of an ongoing hydroelectric project relicensing effort for the Hells Canyon Complex on the Snake River. The Complex includes the lower Boise River as an important tributary. Chandler and Chapman (2001) documented evidence of Chinook salmon spawning in the lower reaches of the lower Boise River until the early 1860s, coincident with the time when mining and irrigation projects began. They also reported steelhead runs in the lower Boise River, as well as the presence of Pacific lamprey (Lampetra tridentatus) in the river near Caldwell.

Within the last century, the lower reaches of the lower Boise River changed from a thriving, cold water fish community with significant numbers of salmon and trout to a cool- and warm-water fish community. Nonindigenous warm-water fishes, including common carp (Cyprinus carpio), largemouth bass (Micropterus salmoides), smallmouth bass (M. dolomieu), bluegill (Lepomis macrochirus), channel catfish (Ictalurus punctatus), tadpole madtom (Noturus gyrinus), and oriental weatherfish (Misgurnus anguillicaudatus) have been introduced into the lower Boise River since the turn of the 20th century (Mullins, 1999a; Chandler and Chapman, 2001). Some of these nonindigenous fish species are known to be detrimental to salmonid populations (Li and others, 1987; Fuller and others, 1999). The Hells Canyon Complex of dams (Brownlee, Oxbow, and Hells Canyon), built between 1959 and 1967, prevented salmonids from entering the lower Boise River (Chandler and Chapman, 2001). Chandler and Chapman (2001) concluded, following the 2001 study, that the lower Boise River was no longer suitable to support salmonid spawning because of high water temperatures (greater than 20ºC) in the late summer.

Benke (1992) designated all native rainbow trout (Oncorhynchus mykiss) in the Columbia River Basin east of the Cascade Mountains, which includes the lower Boise River Basin, as redband trout. The Idaho Department of Fish and Game (IDFG) has not verified that the wild rainbow trout in the lower Boise River are a genetically distinct species (Jeff Dillon, oral commun., November 2005). The American Fisheries Society has grouped redband trout and rainbow trout into one group but does recognize that with additional genetic data this could be revised (Nelson and others, 2004). The IDFG manages the lower Boise River as a “put and take” fishery through the City of Boise (Idaho Department of Fish and Game, 2000). IDFG has created a very popular urban fishery by stocking the river with hatchery-reared rainbow trout of catchable size (greater than 6 in. total length). For example, more than 56,000 rainbow trout were stocked in the lower Boise River in 2004 (accessed June 15, 2006, at In addition, IDFG has stocked Chinook salmon and steelhead in the lower Boise River.

Previous Fishery Investigations

The impairment of water quality and biological integrity in the lower Boise River and several of its tributaries has been evaluated as part of Federal and State monitoring programs, but only a few of those programs included an examination of fish communities (MacCoy, 2004). A summary of U.S. Geological Survey (USGS) and IDFG fish sampling in the lower Boise River since 1974 is shown in table 1, and the location of sampling reaches is shown in table 2.

Idaho Department of Fish and Game, 1974-75

The IDFG conducted a survey of fish populations and water quality in the lower Boise from its mouth upstream to Barber Dam during 1974 and 1975 (Idaho Department of Fish and Game, 1975). The 1974 sampling of 10 reaches (1  through 9 and a reach near Notus, fig. 1) of the lower Boise River was part of the Snake River Fisheries Investigation (a survey of the physical and biological information of the Snake River upstream of Brownlee Reservoir; Idaho Department of Fish and Game, 1975). The lower Boise River was included in the investigation because of its importance to the Snake River drainage. This study was the first extensive assessment of the fish community in the lower Boise River. The IDFG found abundant mountain whitefish populations in the Barber Dam to Star reach. The report concluded that these fish were competing with juvenile and adult trout, and it recommended cropping the population. The IDFG also recommended that this reach be managed as a cold water fishery. The Star to mouth reach was dominated by warm water species (mainly in the sloughs), and the IDFG recommended that the reach be managed as a warm water fishery. They also stated that minimum and maximum flow requirements should be established for the well being of aquatic life (Idaho Department of Fish and Game, 1975).

U.S. Geological Survey, 1988

In 1988, the USGS evaluated the effect of multiple wastewater discharges on water quality and aquatic communities in the lower Boise River (Frenzel, 1988; 1990). The study was designed primarily to assess trace-element effects on aquatic communities. Artificial substrates were used to assess macroinvertebrate communities, and IDFG assisted in the assessment of the fish community by electrofishing reaches 2 through 5 (fig. 1) upstream and downstream of the Lander and West Boise WTFs (reaches 2, 3, 4, and 5; fig.  1). Frenzel (1988) found no evidence of adverse affects of the effluent from these facilities on the macroinvertebrate and fish communities. Asbridge and Bjornn (1988) included information from the USGS study and additional data in a survey of potential and available salmonid habitat in the lower Boise River. They concluded that the lower Boise River was not ideally suited to trout due to high velocities in the upper reaches and high temperature in the lower reaches. Winter cover also was mentioned as affecting trout abundance.

Idaho Department of Fish and Game, 1992 and 1993-94

Population estimates of trout and mountain whitefish were conducted by IDFG during the spring of 1992 and the winter of 1993–94 at reach locations similar to those in 1988 through the City of Boise (Frenzel, 1988). Idaho Department of Fish and Game (2000) noted that sportfish populations continued to decrease, with the most likely cause being the low winter flows.

U.S. Geological Survey, 1995–96

As a follow-up study to the 1988 and 1992 studies, the USGS, in cooperation with the City of Boise, sampled fish communities upstream and downstream of the Lander and West Boise WTFs during the spring of 1995 and the autumn of 1996 (reaches 2 through 5, fig. 1). An IBI was calculated using percentages of sculpin, salmonids, pollution-tolerant species, invertivores, juvenile trout (assumed to be those less than 100 mm total length), juvenile mountain whitefish (assumed to be those less than 210 mm total length), and percentage of individuals with one or more anomalies (Mullins, 1999b). High flows in autumn of 1996 in the lower Boise River affected sampling efforts. Therefore, accurate species abundance estimates could not be made, and this data are not included in this report. The IBI scores were similar among the four sampling reaches, although Mullins (1999b) noted variability between riffles sampled within a reach. He suggested that more frequent sampling would help to determine any statistical differences between reaches. Sculpins were only found upstream of the Lander WTF, with shorthead sculpin (Cottus confusus) being the most abundant species (appendix A). Mullins (1996a) also noted the absence of juvenile trout at all locations, which may have been an indication of poor natural recruitment.

U.S. Geological Survey, 1996–97

The USGS conducted fish-community surveys at five locations (reaches 1, 3, 7, 8 and 9; fig. 1) during December 1996 and August 1997, as part of an ongoing water-quality and biological integrity study done in cooperation with IDEQ and the Lower Boise River Water Quality Plan (Mullins, 1999a). Representative reaches at each location were sampled with both boat and backpack electrofishing equipment. IBI for each reach using five metrics (percentages of sculpin, salmonids, pollution-tolerant species, invertivores, and individual anomalies) were summarized only for the data collected in 1996 (Mullins, 1999a). The 1997 data were of poor quality due to problems associated with high-flow sampling, and those data were not used in the assessment of biotic integrity. The IBI scores calculated for reaches 3, 7, and 9 (fig. 1) in 1996 indicated a longitudinal decrease in biological integrity, with the lowest score from reach 9 near the mouth (fig. 1). At reach 9, the fish community consisted of a high percentage of pollution-tolerant species, a reduced number of salmonids and invertivores, and a relatively high occurrence of anomalies. Mullins (1999a) concluded that the lower Boise River was moderately impaired in the upper reaches, and that river water quality decreased gradually downstream. He described a lack of well-developed pools, riffles, and fish cover, and he also noted extended low winter flow and high summer water temperatures in the lower reaches. Mullins (1999a) recommended monitoring the fish community and habitat in the lower Boise River on a 3- to 5-year cycle.

U.S. Geological Survey, 2001 and 2004

The USGS sampled the fish community at reach 3 (fig. 1) in 2001 and 2004, as part of the Idaho Statewide Water Quality Network. Data from 2001 were summarized in MacCoy (2004), but the data collected in 2004 have not been previously published. The IBI score calculated for reach 3 in 2001 (68) was higher than the score calculated for the 1996 data (57), indicating a possible improvement to the fish community.

U.S. Geological Survey and City of Boise, 2003

In November 2003, the USGS, in cooperation with the City of Boise, conducted another follow-up study of the fish community upstream and downstream of the WTFs. This evaluation included reaches 1 through 5 (fig. 1), and the sampling reaches were extended to 40 times the channel width (about 1 mi long) to capture the maximum fish diversity in each reach as described by Maret and Ott (2003). The 2003 data have not been previously published.

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