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Multiyear drought is projected to increase in frequency and duration in arid and semiarid regions across the world, threatening native species and ecosystem function. The effects of multiyear drought are often exacerbated by human water use for consumption, energy production, and agriculture, which, in lentic ecosystems, manifest in reduced lake elevation and altered habitat for aquatic species. Here, we demonstrate that decreasing lake levels, associated with drought and water management, reduce the availability of littoral cobble habitat to fishes by creating an elevation-explicit littoral habitat map. We combined long-term fish catch data and a lake elevation time series with our elevation-explicit littoral habitat map to test whether fish species population demographics are related to drought-driven changes in littoral habitat. We surveyed the littoral zone of Bear Lake, Utah and Idaho, U.S.A., from full pool to a depth of >12 m, totalling 94.86 km(2) surveyed. As lake elevation decreased >6 m from full pool to the lowest historical elevation, the area of littoral cobble decreased by >97%. Bear Lake sculpin (Cottus extensus, Cottidae), a cold-water fish species which relies on cobble for reproduction, catch per unit effort decreased by >75% with littoral cobble, and year class strength declined by as much as 86%, but varied across age. We predicted the response of age-0 to age-4 sculpin under high and low cobble availability. Our simulations predict a 60%-85% decline in juvenile sculpin CPUE (age-2 and younger) when cobble availability decreases from the 95th to 5th percentile. Our study provided a unique opportunity to identify quantitative linkages between climate-driven littoral habitat loss and an ecologically important profundal fish species, expanding our understanding of potential future pathways through which climate change may affect lentic ecosystems and fishes.