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Although water availability is known to affect landscape‐scale patterns of wildlife diversity and distribution in arid environments, little is known about the microhabitat characteristics that shape the local‐scale distribution of desert bats. We examined the relative importance of pond microhabitat characteristics for the conservation of bats, and hypothesized that in arid environments, patterns of bat diversity and community composition relate to the size of the pond and its hydroperiod (the number of months a pond holds water), a term we use to distinguish between permanent, semi‐permanent and temporary ponds. We combined acoustic monitoring with video recording and an experimental approach to study bat activity over natural ponds in the Negev Desert, Israel. We found that both within and between ponds bat species richness and activity significantly increased with pond size. An experimental reduction of pond …