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.

While many studies have established the importance of streamflow as a driver of fish population dynamics, few have examined relationships between survival of juvenile salmonids and flow‐related variables in intermittent streams. With predictions for a higher frequency of drought conditions due to climate change and the associated increasing human demand for water during the dry season, understanding fish–flow relationships is becoming increasingly important for the protection of sensitive aquatic species. To examine the effects of low streamflow on juvenile salmonids rearing in small intermittent streams, we estimated survival and collected environmental data in four coastal California watersheds from 2011 to 2013. We used an individual‐based mark–recapture modeling approach to evaluate the influence of flow‐related variables on oversummer survival of PIT‐tagged juvenile Coho Salmon Oncorhynchus kisutch stocked into eight stream reaches. Survival was positively associated with streamflow magnitude, wetted volume, and dissolved oxygen and negatively associated with days of disconnected surface flow (days of disconnection) and temperature. Days of disconnection best explained survival, though the relationship varied by geomorphic reach type. Survival was lower in alluvial reaches than in bedrock and clay reaches and showed a faster rate of decline with increasing days of disconnection and drought condition. In all reaches, the onset of pool disconnection represented a turning point at which water quality, water quantity, and survival declined. For this reason, we suggest that days of disconnection (or the flow magnitude at which pools become disconnected) is a useful metric for identifying flow‐impaired reaches, informing streamflow protection strategies, and prioritizing streamflow enhancement efforts designed to benefit sensitive salmonid populations in intermittent streams.

Streamflow depletion is occurring globally, due to land use change, climate change, and increasing human water demand. Ecological effects of low flows are particularly significant for diadromous fish, which require connected stream networks to migrate between fresh and marine waters. In coastal California, USA, drying streams are known to limit rearing habitat for juvenile salmon, but effects on their seaward migration remain poorly understood. In this study, we evaluated the outmigration of endangered, juvenile coho salmon ( Oncorhynchus kisutch) during the late spring flow recession in four streams over 10 years. We monitored the outmigration of fish tagged with passive integrated transponders via detections at stationary antennas, and we measured stream water depths when movement was detected. We assessed depths at multiple riffle crest thalwegs (RCTs), the shallowest geomorphic feature that fish must navigate. Finally, we calculated population-level outmigration depth preferences by evaluating depths during fish movement, relative to depths available during the potential outmigration window. Juvenile fish moved over a wide range of depths (interquartile range 6.1–18.0 cm), which varied by year and stream. Fish ceased to move at shallow water depths, which limited late-season outmigration as stream drying occurred. Our findings suggest that management actions to increase streamflow during the spring would benefit salmon outmigration and could contribute to population recovery. Streamflow-RCT depth relationships, used to assess coho depth preferences during movement, is a relatively simple and effective method for assessing environmental flow needs, a priority for aquatic conservation in California and globally.

In the Western United States, juvenile salmon and steelhead are especially vulnerable to streamflow depletion in the dry season. Releasing water from off-channel storage is a method of streamflow augmentation increasingly used to offset impacts of anthropogenic flow alteration. However, to date, no studies have evaluated the effects of these small-scale flow augmentations on salmonids. Here we quantify the effects of one such augmentation project on habitat connectivity, water quality, invertebrate drift, juvenile salmonid movement and survival. Our study took place in a Northern California stream and included an unusually wet summer (2019) and a more typical dry summer (2020). We found that differences in ambient streamflows between the two years mediated the physical and ecological effects of a 13.9 L/s augmentation treatment. In the dry year, flow augmentation significantly improved dissolved oxygen and habitat connectivity at sites > 1.5 km downstream from the point of augmentation and had a marginal warming effect on stream temperature. During the wet year, both dissolved oxygen and water temperature effects were negligible. In both years, augmentation had a small but positive effect on invertebrate drift. Inter-pool movement of juvenile steelhead (Oncorhynchus mykiss) and stocked Coho Salmon (O. kisutch) increased due to augmentation during the dry summer. Flow augmentation also increased the survival probability for salmonids, with a larger effect during the dry summer (24% higher survival for Coho and 20% higher for steelhead), than during the wet summer (when no effect was observed for steelhead survival and Coho Salmon survival increased by 11%). This study indicates that appropriately designed and timed flow augmentations can improve conditions for rearing salmonids in small streams, particularly during dry years. More broadly it provides empirical evidence that efforts to restore summer streamflow in small, salmon-bearing streams can yield significant ecological benefits.