Climate change, together with the increasing influence of anthropogenic activities in the atmosphere, has impacted ecosystems enormously, escalating much concern for pollution control and management. Proper assessment of the effect of temperature rise due to global warming and the subsequent changes in hydrology on catchment biogeochemical processes is essential for accurate prediction of pollution level. Not many studies have been carried out on the aspect of climate change‐driven nutrient pollution assessment, and inability of many existing modelling tools persists. With these research needs in focus, this study has made an assessment of climate change impact on nutrient pollution by applying a distributed hydrological modelling tool with newly developed nutrient modules that incorporate climate‐based description of catchment and in‐stream processes. The model has been applied to the Latrobe River basin in Australia and calibrated and validated prior to simulation of climate change scenarios. The scenarios have been developed on the basis of the Intergovernmental Panel on Climate Change projections of higher‐emission scenario A1F1 for this region. The model has predicted the impact of temperature rise on the nutrient‐transformation processes and the subsequent releases into waterways for projected high‐flow and low‐flow situations. The results show that climate change is likely to contribute to increase in nutrient pollution in the waterways. The results have been used to assess future stream water quality condition in the study area.