White sturgeon(Acipenser transmontanus) are the largest, freshwater fish in North America. Historically, sturgeon up to 1,500 pounds were caught by anglers. They can live to be over 100 years old! They reside in the Snake, lower Salmon, and Kootenai Rivers of Idaho. They are creatures of large rivers and are uniquely adapted for life on the bottom. Torpedo-shaped bodies help them swim effortlessly in brisk river currents, and their small eyes are adapted for the dark, deep pools where they live. Sensitive whiskers help them identify food items in the dark water, and their suction-tube mouths easily vacuum up whatever food they come across. These fish grew to enormous sizes feeding on the abundant runs of salmon, steelhead, pacific lamprey, and freshwater mussels.

The Kootenai River white sturgeon is 1 of 18 land-locked populations of white sturgeon known to occur in western North America. Kootenai sturgeon occur in Idaho, Montana, and British Columbia, Canada, and are restricted to approximately 167.7 River Mile (RM) of the Kootenai River extending from Kootenai Falls, Montana, located 31 RM below Libby Dam, Montana, downstream through Kootenay Lake to Corra Linn Dam at the outflow from Kootenay Lake in British Columbia. Approximately 45 percent of the species’ range is located within British Columbia. Many Kootenai sturgeon migrate within this restricted portion of the Kootenai River system to spawn in the Kootenai River, and they spend part of their life in Kootenay Lake in British Columbia. The Kootenai River originates in Kootenay National Park in British Columbia, flows south into Montana, northwest into Idaho, then north through the Kootenai Valley back into British Columbia, where it flows through Kootenay Lake and joins the Columbia River at Castlegar, British Columbia. The wild population now consists of an aging cohort of large, old fish. The population has declined from approximately 7,000 white sturgeon in the late 1970s to 760 fish in 2000. At the current mortality rate of 9 percent per year, fewer than 500 adults remained in 2005 and there may be fewer than 50 remaining by 2030. Current data indicate that population abundance declines by about half every 7.4 years. During the last 14 years of intensive monitoring (using techniques proven suitable elsewhere) only one hatching embryo has been found and no free-swimming larvae or young-of-the-year have been captured. Estimates show that annually an average of 10 juvenile sturgeon are naturally reproduced in the Kootenai River. This suggests high levels of mortality which are unlikely to sustain the historic population of Kootenai sturgeon.

Kokanee, Mountain Whitefish, Cutthroat Trout, Rainbow Trout, Book Trout, and Bull Trout can be found swimming around the creeks that pass through the refuge.

Brown bullhead and burbot (ling cod) are present on and around the refuge. In Idaho, burbot are only found in the Kootenai River drainage. Current population estimates of burbot entering Idaho in the fall and winter average <25/year.  Adult burbot primarily inhabit deep lakes or cool rivers or reservoirs in the southern edges of their range year. Although burbot can spawn in lakes and rivers, the population entering Idaho is primarily a spawning population from Kootenay Lake in British Columbia, which leaves the lake in the late fall and early winter to spawn in the Kootenai River or tributary streams in Idaho. In rivers, burbot spawn in low velocity areas in main channels or inside channels behind deposition bars. The preferred substrate is fine gravel, sand or silt. Eggs are broadcast above the substrate. The semi–buoyant eggs may drift but eventually settle into the substrate. Spawning is generally high synchronized over a short 2–3 week time period when water temperatures are low (1–3 C [34–39 F]). Burbot primarily feed at night, with fry feeding on zooplankton and small aquatic invertebrates. As they grow, their diet changes to include fish. As adults more than 80% of their diet is likely to be fish.

Two species of sculpin may be found in the waters on the refuge, Slimpy and Torrent Sculpin.  The torrent sculpin(Cottus rhotheus) is a freshwater sculpin. Like most cottids, the torrent sculpin is a benthic species characterized by large, rounded pectoral fins, a large, flattened head with dorsal eyes, and a body and head frequently covered with spines or prickles (Moyle and Cech 1996). The torrent sculpin is gray-brown with black speckling and has a heavily mottled chin and has two forward-slanting, dark bands on both sides of its body under the soft, posterior portion of the dorsal fin.

The slimy sculpin, Cottus cognatus, is a freshwater species of fish that inhabits cool, rocky streams, rivers and lakes throughout northern North America and eastern Siberia.  The slimy sculpin is found in freshwater and sometimes brackish water in areas with rocky or gravel type bottoms. The slimy sculpin is a nocturnal fish that usually spends most of its time on the stream bottom and seeks shelter under rocks and logs, especially during spawning season. When it swims, it sometimes appears to be “hopping” along the bottom because of its inefficient ability to swim. This is partly due to the absence of a swim bladder, which normally gives buoyancy to a fish.