Nonpoint pollution from agriculture is an important environmental policy issue in Spain and the European Union. Agricultural pollution in Spain is being addressed by the National Irrigation Plan and by the European Water Framework Directive. This article contributes to the ongoing policy decision process by analyzing nonpoint pollution control and presenting results on the efficiency of abatement measures. Results question the reliance of the Water Framework Directive on water pricing as a pollution instrument for reaching good status for all waters because higher water prices close to full recovery cost advocated by the directive appear to be inefficient as an emission control instrument. Another important result is that abatement measures based on input taxes and standards on nitrogen appear to be more suitable than the National Irrigation Plan subsidies designed to promote irrigation investments. The results also contribute with further evidence to the discussion on the appropriate instrument base for pollution control, proving that nonpoint pollution control instruments cannot be assessed accurately without a correct understanding of the key underlying biophysical processes. Nonpoint pollution is characterized by nonlinearities, dynamics, and spatial dependency, and neglect of the dynamic aspects may lead to serious consequences for the design of measures. Finally, a quantitative assessment has been performed to explore discriminating measures based on crop pollution potential on vulnerable soils. No significant welfare gains are found from discriminating control, although results are contingent upon the level of damage, and discrimination could be justified in areas with valuable ecosystems and severe pollution damages.