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In dryland rivers, flow intermittency means fish populations are often subjected to drought disturbance. The viability of these fish populations depends on the availability of waterhole refuges for individuals to survive drought (resistance) and the ability of surviving fish to repopulate the rivers by recruitment and dispersal once flow returns (resilience). In this study we combined remote-sensed mapping of the locations of waterholes that lasted through an extreme drought in the northern Murray Darling Basin, Australia, with an assessment of the impacts of in-stream barriers on limiting the opportunities for fish to move and repopulate after drought. We found that at the peak of this 2018–2020 drought, the worst on record for some rivers and the most spatially synchronous recorded across the region, waterholes were few and generally small – representing only 11% of the total river channel network. All the fish in the region that survived the drought were concentrated into this limited waterhole refuge habitat. Even small instream structures, such as minor weirs, caused large reductions in the opportunities for fish to move between river segments when there is flow. Almost all the 104 instream structures assessed reduced long-term fish movement opportunities, measured as days with discharge greater than calculated barrier drown out thresholds, by more than 70% and up to 100%, when compared to opportunities for movement if the barrier was not present. This large impact from small instream barriers is a consequence of flow intermittency and is likely to reduce fish population resilience and impact the capacity of fish populations to recover after drought. Combining information on the risks posed by limited refuge habitat availability during drought and from reduced movement opportunity following drought allowed us to identify river segments where these combined threats are the greatest risk to viability of local fish populations. Considering the spatial arrangements of these risks provides a means to systematically prioritize mitigation measures such as weir removal to improve fish movement opportunities and local management of key waterholes to increase drought resistance. The approach used here provides a guide for assessing and prioritizing the management of fish population viability risks from drought and fragmentation by barriers in any non-perennial river setting.

Risks to Fish Populations in Dryland Rivers From the Combined Threats of Drought and Instream Barriers