Eutrophication of rivers and receiving waters has become a major environmental issue worldwide, which may further intensify due to projected climate changes and expansion of urbanization or agricultural development to meet the needs of increased human population. However, our understanding of climatic and land use change impacts on riverine nutrient retention and export to receiving waters is limited due to lack of empirical measurements and uncertainties about the nature of future climate changes. The aim of this paper is to analyze the response of nitrate transport and transformation in river systems to potential changes in climate and land use management, individually, and in combination. A coupled hydrological and biogeochemical model is implemented in a hypothetical river basin, with realistic inputs and parameters, for the simulation of nitrate dynamics in river networks. Results indicate that for the same annual rainfall, increased within‐year rainfall variability propagates to increased streamflow variability and a significant reduction in nitrate retention. Analysis of the effects of the spatial distribution of nitrate inputs around the river network showed that for the same total nitrate input from land, nitrate retention increased considerably through locating land use types with high nitrate input away from the river outlet. Simulation results also indicated that even without a reduction in total nitrogen input from land, optimized land use distribution around the river network can compensate the enhanced nitrogen input that may arise from increased rainfall variability. These findings offer viable strategies for catchment management to mitigate increased water quality degradation caused by expected future climate changes.