Pressures on freshwater ecosystems are mainly human induced and driven by land use and climate change. We develop an empirical framework to estimate the impacts of land use (agriculture, forest, pasture, urban) and climate change on freshwater biodiversity, measured by a fish-based index, in France. Our estimation results reveal that rivers in areas with more intensive agriculture and steep pasture are associated with lower freshwater biodiversity compared with forest areas. Our simulations show that climate change will exacerbate these negative impacts through land use adaptation. We discuss how two command-and-control policies could help improving freshwater biodiversity and cope with the adverse effects of land use and climate change.