This study is the first to estimate the effect of Agri-Environmental Schemes (AES) on nutrient runoff using abatement data and water samples on a large scale. This unique combination of data sources identifies all farms located upstream from a given water sampling site. By using watersheds that cover 91% of the Swedish land area and AES payments to 83% of Swedish farms, the study is almost a full population evaluation. A watershed fixed-effect model estimates whether within-watershed variation in AES payments affects nitrogen and phosphorus concentrations in water samples. For the period 1997–2013, the study finds that higher uptake of the AES Wetland, Catch crop/No autumn tillage, Environmental protection measures and Culturally significant landscape elements was associated with reduced nutrient runoff. However, uptake of Grassed buffer zones, Pastures and meadows and Organic production was associated with increased nutrient runoff.