A large amount of variability exists in the health of fish communities in the upper Snake River Basin. In some streams of the basin, cutthroat, rainbow, and brown trout fisheries represent some of the highest quality fishing in the Nation. In other areas of the basin, where streams have been degraded by land- and water-use activities, the fish community is composed of warmwater-tolerant, nongame species. Because trout species generally require cold water temperatures and ample dissolved oxygen for survival, trout species have been nearly eliminated in several degraded streams of the basin [6,7].
Fishing enthusiasts from all parts of the Nation enjoy the high-quality fisheries in some headwater areas of the upper Snake River Basin. Large cutthroat, rainbow, and brown trout, like this one caught from the Henrys Fork, are typical of fish communities in the Henrys Fork and the Snake River upstream from its confluence with the Henrys Fork. Although healthy trout populations once existed in all parts of the basin, today they are located primarily in pristine headwater areas of the basin (photograph © 1996 by W.H. Mullins and published with permission).
Characterization of fish communities in streams and reservoirs is a useful tool for assessing effects of land- and water-use activities on water-quality conditions because fish are sensitive to a large array of stresses, many species of fish are widely distributed, and descriptive analyses of fish communities are easy to understand. Fish are also relatively long-lived, and they integrate adverse effects of stresses in the aquatic community. In addition, Idaho water-quality standards designate aquatic biota and salmonid spawning as beneficial uses of many streams in the State and, as a result, water-quality criteria have been established to protect instream fisheries. Specific areas of concern include input of chemical pollutants, loss of instream habitat, sedimentation of spawning beds, decreased streamflows, increased water temperatures, and introduction of non-native species [7].
Overall, 26 native and 13 introduced fish species representing numerous different fish families were collected in the basin during the NAWQA study. About 73 percent of the species collected from all sites were native [6]. An Index of Biotic Integrity derived from NAWQA data indicates that, in general, the quality of fish communities in the Snake River and its tributaries deteriorates from the headwaters of the Snake River near Yellowstone National Park to the basin outlet at King Hill. The notable exception to this trend is in Rock Creek near Twin Falls, where fish stocking and the inflow of sediment-free ground water results in a fish community of better quality than that of many upstream sites.
A common perception about fish communities is that, the greater the number of fish species and the greater the number of total fish, the better the stream-water quality. Usually, a diverse community with many species indicates good water quality. Polluted water, on the other hand, generally contains fewer species, many of which can tolerate pollution and procreate rapidly. Although this perception may be true in some areas of the Nation, it is not necessarily true for fish communities in coldwater streams of Idaho and Wyoming [14].
In the upper Snake River Basin, high-quality streams at high elevations usually contain fewer fish species than do streams at lower elevations [6]. Many headwater streams might have been devoid of fish prior to the introduction of selected species for sportfishing. Coldwater streams generally do not offer the food sources, temperature, and habitat features that many fish species prefer. Fish community sampling during the NAWQA study and historical data from the upper Snake River Basin indicate that relatively small, undisturbed headwater streams in northern, eastern, and southern parts of the basin tend to contain the fewest fish and the lowest number of species. Numerous small reference (least disturbed by human activities) streams in the basin contained an average of only 2 to 4 fish species and less than 100 total fish in the reaches sampled. In most of the reference streams sampled, only native or introduced trout and sculpin were present. In contrast, streams with degraded water quality contained between 5 and 10 different fish species and greater numbers of fish than reference streams contained. Fish communities in degraded streams were predominantly introduced, nongame species tolerant of degraded water-quality conditions.
The upper reaches of the Henrys Fork and the Snake River upstream from its confluence with the Henrys Fork represent two of the best large-river trout fisheries in the Nation. Cutthroat, rainbow, and brown trout make up most of the game species in these stream segments. Nongame species are primarily native sculpin and suckers. Rainbow and brown trout, introduced to enhance the sportfishery, make up most of the non-native species in the upper reaches of the Henrys Fork and the Snake River upstream from the confluence.
Downstream from the confluence of the Snake River and Henrys Fork to Milner Dam, fish communities in the Snake River and its major tributaries are composed primarily of cutthroat trout and other native and non-native species [7]. However, fish communities in this reach have been degraded by the cumulative effects of irrigation return flows, grazing, and diversions. Sediment from bank erosion and irrigation return flows has blanketed stream bottoms and caused loss of suitable spawning habitat. Reservoirs and irrigation diversions in the reach also have resulted in reduced streamflows, degraded water-quality conditions, loss of habitat, and proliferation of non-native, warmwater species of fish [7].
Historical information indicates that, prior to hydroelectric power development, numerous native, ocean-migratory species inhabited the Snake River from Shoshone Falls near the city of Twin Falls downstream to the basin outlet at King Hill. Species included chinook salmon, steelhead, Pacific lamprey, and white sturgeon [7]. Of these species, only the white sturgeon is still present in the reach, but the population is declining and is sparsely distributed. Fish community assessments conducted during the NAWQA study indicate that this reach of the Snake River is composed predominantly of nongame species such as carp and suckers [6]. The presence of a fish community dominated by carp and suckers is attributable to reduced streamflows, large inputs of nutrients and fine-grained sediment, excessive aquatic plant growth, and elevated water temperature. Temperatures in excess of 19 degrees Celsius (the maximum criterion for coldwater biota) and dissolved-oxygen concentrations as small as 1.0 milligram per liter have been measured [7]. Because of the degraded water quality, trout have been nearly eliminated in the reach of the Snake River between Shoshone Falls and King Hill.
