Several studies have analysed the effects of European environmental policies on water quality, but no detailed retrospective analysis of the impacts of the Common Agricultural Policy (CAP) reforms on observed water quality parameters has been carried out. This study evaluates the impact of the CAP and other drivers on the concentrations of nitrates and suspended solids in the Guadalquivir River Basin (southern Spain) over the 1999-2009 period. The most important drivers that are degrading both water quality indicators are exports from upland areas and agricultural intensification. Water quality conditions have improved in regions where there has been abandonment and/or deintensification. The decoupling process has reduced the concentration of nitrates and suspended solids in a number of subbasins. Although agricultural production and water efficiency in the basin have improved, high erosion rates have not yet been addressed.