Climate change is one of the main drivers of biodiversity decline. Rapidly changing climate in the form of warming, drying, and habitat isolation causes freshwater species to change their spatial extent, as most species have little capacity for in situ responses. However, the relative contribution of these three effects to freshwater species' changing spatial distributions is actively debated. To shed light on this debate, we explored temperature, hydroperiod, and habitat connectivity effects on alpine pond species occupancy probabilities in the northern French Alps. We studied alpine ponds as ideal test systems because they face climate change effects more rapidly, and in more concentrated areas, than any other freshwater ecosystem. We used multispecies occupancy models with three biological groups (amphibians, macrophytes, and Odonata) to examine contrasting responses to climate change. Contrary to expectations, temperature was not the main driver of species occupancy probabilities. Instead, hydroperiod and connectivity were stronger predictors of species occupancy probabilities. Furthermore, temperature increases had the same effect on occupancy probabilities of non-alpine specialist and alpine specialist species. Nonetheless, temperature disproportionately affected a greater number of specialist species compared with non-alpine specialists. We conclude that climate change mitigation will primarily benefit a greater number of alpine specialist species than non-alpine specialists. Finally, we suggest that enhancing our understanding of freshwater hydroperiods will improve our predictions of climate change effects on freshwater species distributions.