When designing and implementing agri-environmental policies to reduce nutrient loss, action programmes may falsely address areas where the nutrient issue from agricultural activity is not currently important and is not likely to become so in the future (a false positive), or may fail to address areas where the agricultural nutrient issue is currently important or may likely become so in the future (a false negative). Based on a case study of the Louros watershed in Greece, this work identifies database and modelling sources of false positives and negatives and proposes a decision making process aimed at minimizing the possibility of committing such errors. The baseline is well simulated and shows that the Louro's watershed falls behind a Good Environmental Status, at least marginally. Simulated mitigation measures show that the river's status can be upgraded to "Good", at least as concerns nitrates and ammonium. Simulated climate change does not seem to exert an important positive or negative effect. Land use changes forecasting considerably less cultivated area have a significant effect on Total Phosphorous but not on nitrates or ammonium concentrations. The non-linearity between nutrient disposition (inputs) and nutrient concentration in downstream water bodies (output) and the many factors that affect the nutrient disposition-transportation-concentration chain, highlights the importance of simulating the effects of mitigation actions and of future climate and land use changes before adopting and establishing agri-environmental measures. (C) 2016 Elsevier B.V. All rights reserved.