Perennial rivers and streams make a disproportionate contribution to global carbon (C)cycling. However, the contribution of intermittent rivers and ephemeral streams, which

1. In river systems, aquatic invertebrate communities are surprisingly persistent over time and generally recover quickly from disturbances. Drift has long been viewed as the primary process promoting this resilience, and it plays a important role in predictive models of community composition and concepts in lotic ecology. More recently, other processes such as vertical migration from the hyporheic zone, aerial oviposition from distant refuges and the use of resistance forms (e.g. diapause) have received greater recognition and support for their importance. 2. In this study, the view that drift is the primary process promoting invertebrate community resilience was challenged in an intermittent alluvial river using reach-scale flow manipulations. First, six treatment channels were completely dried for 1 week, while three others were left flowing to be used as controls. Second, flow was re-established in channels and drift was either allowed or blocked for a 4-week period. Third, during this period the resilience of community structure, composition and function was compared between treatments, and the potential for colonisation from the drift, hyporheic zone, aerial oviposition and resistance forms was measured. 3. Communities recovered after only 2 weeks in all of the previously dried channels, and contrary to our hypotheses, invertebrate community structure, composition and functional trait composition were not altered by blocking drift, indicating it was not the primary process promoting resilience in this river. 4. Three lines of evidence suggested colonisation from the hyporheic zone and not aerial oviposition nor resistance forms promoted resilience following rewetting including the following: (i) finding all common benthic taxa in the hyporheic zone during the drying event, (ii) a distinct decrease in invertebrate size upon rewetting in all treatment channels and (iii) a negative correlation between resilience and water table depth. 5. This experiment highlighted the potential importance of the hyporheic zone as a key source of colonisation in alluvial rivers and emphasises the need for a three-dimensional perspective when considering community resilience in rivers. Adaptive management approaches are needed to direct attention to sources (e.g. hyporheic zone) that are essential to promoting community resilience in rivers facing increased pressures due to climate change, water abstraction and flow regime alteration.

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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.