The effective aridity in riparian areas is increasing from climate change and from human water consumption, which exacerbates the impacts of effluents from wastewater-treatment plants and from catchment run-off in rivers. The potential of natural riparian areas to act as 'green filters' has long been recognized, but the possible ecological benefits of natural riparian areas over large-scale environmental gradients on fish have not been explored in detail. Using an extensive data-set from northeastern Spain (99,700 km2, 15 catchments, 530 sites), ours is the first study to ask whether natural riparian vegetation can mitigate the effects of pollution on fish in rivers experiencing water scarcity. We used multimodel inference to explore the additive and interactive effects of riparian vegetation with nutrient pollution and water conductivity, which are among the world's worst river stressors, on multiple fish guilds, including widely distributed species and highly invasive alien fish species. Most models (54%) supported the additive effects of water-quality factors on fish, after having accounted for the influence of geography and hydrological alterations. Although many fewer models (7%) included riparian vegetation as an important predictor, riparian vegetation modulated the forms of the associations between fish and pollution. The relationship of nutrient pollution with native and alien fish richness changed from negative to positive with greater riparian structure or species richness. However, we found the opposite effect for the mean body size of sedentary fish, and only positive additive effects of riparian richness for the probability of occurrence of pelagic fish. Ammonium and nitrite concentrations adversely affected fish in these rivers up to 10 years after the enforcement of the implementation of the Water Framework Directive by the European Union. High conductivity also much affects fish, having negatives associations with migratory, pelagic, invertivorous and native fish, and positive associations with sedentary, benthic, omnivorous and alien fish. Therefore, the current status of natural riparian areas is unlikely to fully mitigate water-quality impacts on fish. The conservation of freshwater resources in semi-arid regions, such as north-eastern Spain, requires improved waste-water treatments and better agriculture practices.