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, the CIMaE project (Climatic Impact on Mountain aquatic Ecosystems) aims to explore temperature, hydroperiod, and habitat connectivity effects on alpine pond species occupancy probabilities in the Northern French Alps for defining efficient management strategies to mitigate the effects of climate change. 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 contrasting responses to climate change. We will present the results and their implications for the next phases of the CIMaE project.