Since the mid 1980s, freshwater ecosystems have experienced larger declines in biodiversity than terrestrial and marine ecosystems. Pressures on freshwater ecosystems are mainly human-induced and driven by land use changes. The objective of this paper is to evaluate how land-use adaptation to climate change affects freshwater ecosystems in France. For this purpose, we use data on land use shares (agriculture, pasture, forest and urban) and on an indicator of the ecological status of surface water, namely a fish-based index (FBI) measured for various French rivers observed between 2001 and 2013. We estimate two models: a spatial econometric land use share model and a statistical spatial panel FBI model. The land use share model describes how land use is affected by economic, physical and demographic factors, while the FBI model explains the spatial and temporal distribution of the FBI score by land use and pedo-climatic variables. Our estimation results indicate that land-use adaptation to climate change reduces freshwater biodiversity. We use our estimation results to analyze how two command-and-control policy options could help France to comply with the EU Water Framework directive and mitigate the adverse impacts of climate change on freshwater biodiversity.