Under persistent eutrophication of European water bodies and a changing climate, there is an increasing need to evaluate best‐management practices for reducing nutrient losses from agricultural catchments. In this study, we set up a daily discharge and water quality model in Hydrological Predictions of the Environment for two agricultural catchments representative for common cropping systems in Europe's humid continental regions to forecast the impacts of future climate trajectories on nutrient loads. The model predicted a slight increase in inorganic nitrogen (IN) and total phosphorus (TP) loads under RCP2.6, likely due to precipitation‐driven mobilization. Under RCP4.5 and RCP8.5, the IN loads were forecasted to decrease from 16% to 26% and 21%–50% respectively, most likely due to temperature‐driven increases in crop uptake and evapotranspiration. No distinct trends in TP loads were observed. A 50% decrease in nutrient loads, as targeted by the European Green Deal, was backcasted using a combination of management scenarios, including (a) a 20% reduction in mineral fertilizer application, (b) introducing cover crops (CC), and (c) stream mitigation (SM) by introducing floodplains. Target TP load reductions could only be achieved by SM, which likely results from secondary mobilization of sources within agricultural streams during high discharge events. Target IN load reductions were backcasted with a combination of SM, fertilizer reduction, and CC, wherein the required measures depended strongly on the climatic trajectory. Overall, this study successfully demonstrated a modeling approach for evaluating best‐management practices under diverging climate change trajectories, tailored to the catchment characteristics and specific nutrient reduction targets.