In the Genii River Basin (southern Spain), agriculture is the greatest pressure on freshwater demand. Furthermore, water degradation caused by soil erosion is becoming a key environmental concern. This study aims to assess the water-related impacts of agriculture combining the use of an ecohydrological model (SWAT) with a spatiotemporal water footprint assessment to evaluate the current status of streamflow (blue water), soil water (green water) and the assimilability of sediments by streamflow (grey water footprint). The Common Agricultural Policy (CAP) requires farmers to adopt certain agricultural practices that are beneficial for the environment. Such practices could affect the conditions of available land and water resources. Because of the importance of applying the best land management practices for the maintenance of sustainable water resources, the study also infers probable water availability and water pollution level changes under different post-2013 CAP scenarios. The Genii streamflow is highly regulated, and, as a result, it is hard to discern significant changes (p < 0.05) under the proposed scenarios. However, there is a shift with afforestation measures from unproductive (i.e., direct soil evaporation) to productive water (i.e., evapotranspired water from agricultural and natural areas, excluding non-growing periods) consumption. The probability of annual evapotranspiration from natural areas being greater in afforestation scenarios than in the baseline scenario is 0.70 to 0.88, whereas the likelihood of soil water evaporation being lower is 0.60. Evapotranspiration in natural areas increases by about 521% from September to May under afforestation measures compared with the baseline scenario, whereas soil water evaporation decreases by 30% in winter. The grey water footprint and water pollution level decrease by 19% and 9%, respectively, with the highest streamflow conditions under afforestation as opposed to current conditions. However, water pollution levels of suspended solids greater than 1 indicate that the river flow is not capable of assimilating the existing sediment loads. Since land use changes and agricultural practices have a major impact on water resources, the post-2013 CAP reform can provide environmental benefits for water allocation and mitigation of water pollution. However, further efforts are required to better align the policy goals of the CAP and the Water Framework Directive. (C) 2016 Elsevier Ltd. All rights reserved.