In the north rim of the Mediterranean region, where forest cover is increasing as a result of land abandonment and temperatures are rising as a result of climate change, there is increasing interest for the effects of such changes on the runoff of water courses. This is a paramount issue for the conservation of many freshwater habitats and species. In this work westudied the effects of both an increase in forest cover after depopulation and land abandonment and an increase in temperature on the runoff of a Mediterranean catchment and on the aquatic and semi-aquatic fauna species of the stream (Olzinelles valley, NE Spain). Although in our simulation no decreasing trend in runoff is detected, the monthly runoff-rainfall ratio is now 15% lower than 30 years ago, a fact that may be attributed to a drier period rather than to the small afforestation experienced by the catchment in the last decades. Other factors such as increasing temperatures, changing rainfall patterns and increasing canopy cover are discussed. The observed decrease in the water flow has caused the disappearance of white-clawed crayfish (Austropotamobius pallipes), Mediterranean barbel (Barbus meridionalis), chub (Squalius cephalus), European eel (Anguilla anguilla), and southern water vole (Arvicola sapidus). Our results suggest that in a progressively warmer climate, and especially after land abandonment processes, management of Mediterranean mountain areas should be oriented towards an appropriate distribution of agrarian and forest land-covers in terms of water availability. Down to the stream scale, the pools that keep water throughout the year should be conserved and extended to enhance its potential to maintain aquatic and semi-aquatic species populations.