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Pursuant to the Northwest Power Planning Council's Fish and Wildlife Program for the Columbia River system, we estimated losses in fish populations and developed mitigation, compensation, and protection alternatives for reservoirs and downstream river reaches affected by hydropower development in the Flathead and Kootenai River systems in northwest Montana, U.S.A. The construction of Hungry Horse Dam has resulted in estimated annual losses of 65500 migratory juvenile westslope cutthroat and 1965 adult migratory bull trout from the Flathead Lake and River system. In addition, operations of Hungry Horse and Kerr dams caused annual losses conservatively estimated at 96300 river-spawning and 131000 lakeshore-spawning kokanee adults. Water level fluctuations caused by dam operations at Libby and Hungry Horse reservoirs result in: (1) altered thermal stratification, (2) indirect losses in phytoplankton and zooplankton production, (3) direct washout of phytoplankton and zooplankton through dam penstocks, (4) reductions in standing crop of benthic organisms and of insects on the water surface, and (5) reduced fish growth in the late summer and fall. Mitigative measures include: (1) 99.2 and 113.3 m3 s−1 minimum flows in the Flathead and Kootenai rivers respectively, to protect salmonid eggs and juveniles, (2) improvement of fish passage to restore migrations between the Flathead and Swan systems, and (3) biological rule curves for operations at Libby and Hungry Horse reservoirs. To compensate for fisheries losses, we recommend enhancement of spawning and rearing habitat, introductions of hatchery juveniles, and spawning channels. We recommend protection from further hydropower development for 100 stream reaches (1386 km) for fish species of special concern, and for outstanding sport fisheries. These and other measures will be considered by various agencies in developing an overall fisheries restoration plan which should be flexible, and employ principles of adaptive management. Effectiveness of the plan may be limited by heavy reliance on hatchery fish. Although mitigation efforts may not restore fish populations to pre-dam levels, substantial benefits should be realized. [ABSTRACT FROM AUTHOR]

Kokanee (Oncorhynchus nerka) provided an important recreational fishery in the Flathead River-Lake system (Columbia River Basin, U.S.A.-Canada) until the late 1970s when populations declined dramatically. The declines coincided with peaking river discharge from Hungry Horse Dam during the autumn spawning period and an increase in the duration of lake drawdown caused by the operation of Kerr Dam on the outlet of Flathead Lake. Redds of both river and lakeshore spawners were, therefore, dewatered in winter, causing high freezing and desiccation mortality of eggs during the incubation period. It appeared that growth rates of kokanee were density dependent. Female kokanee from strong year classes (i.e., those produced during years of favourable water levels and flow conditions during the incubation period) were smaller than those from weak year classes when unfavourable conditions for incubation prevailed. A highly significant relationship (r2 = 0.929, p < 0.001) was demonstrated between female kokanee spawner length, river gauge heights, and lake levels during years which produced each year class. The close fit of the relationship was further validated by the strong correlation (r = 0.964) between actual kokanee lengths and predicted lengths. Other factors which could have influenced kokanee year class strength include hatchery plants of kokanee fry, harvest of kokanee by anglers, variations in the carrying capacity of Flathead Lake, and natural fluctuations in egg and fry mortality. [ABSTRACT FROM AUTHOR]