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Stream drying, especially in the western United States, is becoming more common as the climate warms and precipitation patterns become less predictable; consequently, fisheries managers need to prioritize conservation efforts where water (and fish) will persist in the future. Yellow Creek in the upper Bear River watershed (Utah and Wyoming) contains one of the largest remaining populations of Northern Leatherside Chub Lepidomeda copei, an imperiled fish. Lower reaches are drying during summer months, partly due to water withdrawals, thus reducing Northern Leatherside Chub populations and relegating the remaining fish to isolated pools until the water returns. This study used an unmanned aerial vehicle to capture high‐resolution and spatially explicit imagery over 19 km of Yellow Creek in a few weeks during late August when the water is the most limiting to the fish. Through imagery and subsequent GIS analysis, we identified 405 previously unknown potential refuge‐pool habitats for Northern Leatherside Chub and determined their location, size, and spatial distribution, thereby helping managers prioritize stream reaches for native fish conservation and restoration. While the cost of unmanned aerial vehicle flights was estimated to be 2.5 times that of on‐the‐ground surveys in 2016, unmanned aerial vehicle technology continues to become more cost effective and, unlike traditional surveys, provides high‐resolution and spatially referenced data.