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Recent droughts raise global concern over potential biodiversity loss and mitigating impacts to vulnerable species has become a management priority. However, drought impacts on populations are difficult to predict, in part, because habitat refuges can buffer organisms from harsh environmental conditions. In a global change context, more extreme droughts may turn previously suitable habitats into ecological traps, where vulnerable species can no longer persist. Here, we explore the impacts of California's recent record-breaking drought on endangered juvenile Coho salmon. We estimated the variability of cumulative salmon survival using mark-recapture of nearly 20,000 tagged fish in intermittent stream pools during a 7-year period encompassing drought and non-drought conditions. We then determined the relative importance of physical habitat, streamflow, precipitation, landscape, and biological characteristics that may limit survival during drought. Our most striking result was an increase in the number of pools with reduced or zero survival during drought years and a coincident increase in spatial variability in survival among study reaches. In nearly half of the stream pools, salmon survival during drought was similar to mean survival of pools assessed during non-drought years, indicating some pools had remarkable resistance (ability to withstand disturbance) to extreme drought. Lower survival was most attributable to longer duration of disconnection between upstream and downstream habitats, a consequence of increasing drought severity. Our results not only suggest that many pools sustain juvenile salmon in non-drought years transition into ecological traps during drought but also highlight that some pools serve as refuges even under extreme drought conditions. Projected increases in drought severity that lead to longer droughts and greater habitat fragmentation could transform an increasing proportion of suitable habitats into ecological traps. Predicting future impacts of drought on Coho salmon and other sensitive species will require identification and protection of drought refuges and management strategies that prevent further habitat fragmentation.