Understanding how the spatial distribution of ecological resources shape species’ diversity and abundance in human-modified landscapes is a central theme in conservation biology. However, studies often disregard that such patterns may vary over time, thereby potentially missing critical environmental constraints to species persistence. This may be particularly important in highly mobile species such as bats, which are able to track temporal variations in spatial resource distribution. Here we test the hypothesis that bats in Mediterranean landscapes are strongly affected by the progressive reduction in water availability during the seasonal summer drought. We analysed the effects of landscape composition and structure on bat diversity and activity, during Pregnancy, Lactation and Post-lactation periods, and identified the most influential variables within and across periods. Water bodies showed the strongest positive effect on bats, followed by riparian habitats and areas with steeper (>30%) slopes. However, while during Pregnancy there were only small landscape effects, these increased during Lactation and Post-lactation, highlighting a progressively stronger association with water habitats during the summer drought. The spatial projection of habitat models showed that the landscape distribution of bat diversity and activity hotspots changed markedly over time. During Pregnancy the spatial pattern of hotspot distribution was weakly defined, while during Lactation and particularly Post-lactation there was a concentration of hotspots along permanently flowing watercourses. Our study highlights that permanently flowing watercourses are critical for bat conservation in Mediterranean landscapes, calling for measures to counteract their ongoing degradation due in particular to climate change, water abstraction and damming. More generally, our study underlines the importance of considering the temporal dimension in habitat selection studies, without which there is the risk of overlooking the importance of habitats that are key for species persistence only at certain times of the year.