Currently, climate change is considered as an important factor affecting nutrient loads introduced through riverine systems into the Baltic Sea. Although the prospect of a large increase in pollution has long seemed very real, it still does not translate into planning of effective remedial actions. One of the factors limiting the development of such activities is the scale of simulations, focusing generally on catchment outlet profiles. To fill this gap and enable a step forward in understanding responses towards future predictions in a higher resolution scale (subcatchment), we assessed nutrient load contribution using calculation profiles localised along a main watercourse and its tributaries. To track spatial and seasonal changes of total nitrogen and phosphorus under short- and long-term (RCP4.5 and RCP8.5) climate change scenarios we used the digital platform Macromodel DNS/SWAT. Having at our disposal a catchment model with a good performance we could follow not only total load changes in particular subcatchments, but also track localisation of the pollution sources and their direct impact on load estimations. Our results showed an increase of the loads, especially from the agricultural landuse type, up to 34% for TN and 85% for TP in the most extreme scenario. Moreover, forest areas have been noted as highly reactive to the climate changes, and through their localisation able to distinctly alter nutrient outflow. Finally, the contribution of urban areas should be further investigated since the dynamics of nitrogen and phosphorus release from impervious surfaces is noticeably different here than from the other diffuse sources.