Climate change is one of the main drivers of species erosion. 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 situresponses. However, the relative contribution of these three effects to freshwater species’ changing spatial distributions is largely 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 multi-species occupancy models with three biological groups (amphibians, macrophytes and Odonata) to examine contrasted 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 increase had the same effect on occupancy probabilities of generalist and cold-specialist species. Nonetheless, temperature disproportionately affected a greater number of specialist species compared to generalists. We conclude that climate change mitigation will primarily benefit a greater number of specialist species than generalists. Finally, we suggest that enhancing our understanding of freshwater hydroperiods will improve our predictions of climate change effects on freshwater species distributions.