Excessive nutrient loadings into rivers are a well-known ecological problem. Implemented mitigation measures should ideally be cost-effective, but perfectly ranking alternative nutrient mitigation measures according to cost-effectiveness is a difficult methodological challenge. Furthermore, a particularly practical challenge is that cost-effective measures are not necessarily favoured by local stakeholders, and this may impede their successful implementation in practice. The objective of this study was to evaluate the cost-effectiveness of mitigation measures using a methodology that includes a participatory process and social learning to ensure their successful implementation. By combining cost data, hydrological modelling and a bottom-up approach for three different European catchment areas (the Latvian Berze, the Swedish Helge and the German Selke rivers), the cost-effectiveness of 16 nutrient mitigation measures were analysed under current conditions as well as under selected scenarios for future climate and land-use changes. Fertiliser reduction, wetlands, contour ploughing and municipal wastewater treatment plants are the measures that remove nutrients with the highest cost-effectiveness in the respective case study context. However, the results suggest that the cost-effectiveness of measures not only depends on their design, specific location and the conditions of the surrounding area, but is also affected by the future changes the area may be exposed to. Climate and land-use changes do not only affect the cost-effectiveness of measures, but also shape the overall nutrient loads and potential target levels in a catchment.