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The Kootenai River white sturgeon Acipenser transmontanus has been isolated from other white sturgeon populations for over 10,000 years, Bonnington Falls in British Columbia, Canada, creating the isolation. Libby Dam, constructed in 1972, modified the flow and temperature regime of the river, which affected spawning and recruitment of white sturgeon. Kootenai River white sturgeon are only known to spawn in a reach near Bonners Ferry, Idaho, 100 km downstream from the dam. In 2 of 8 years of study, only 15 white sturgeon eggs were collected over gravel–cobble substrate. However, in the other 6 years, 1,193 eggs were collected over sand substrate; these areas usually exceeded 5 m in depth, were within the main channel, and had water velocities of 0.2–1.0 m/s and temperatures of 8.5–12°C. In general, these characteristics differed from optimum white sturgeon spawning habitat in the Columbia River, where velocities average 0.8 m/s, water temperatures are 12–17°C, and gravel–cobble substrate is available. Spawning over sand substrate might contradict survival strategies because white sturgeon have an adhesive egg to which sand adheres. Differences in spawning habitat may be an outcome of behavioral divergence or disruption to environmental cues but was probably caused by preferred habitat no longer being available. Recovery of Kootenai River white sturgeon will depend primarily on continuation of mitigated flows for spawning migrations, suitable spawning habitat, and ultimately survival of eggs and larvae. It is unknown at this time whether recent spawning alone will lead to sufficient recruitment to help recovery of the population, but if it does not recruit substantial year‐classes, we believe consideration must be given to measures that would provide coarser spawning substrates and warmer water temperatures.

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