The study analysed the transboundary Pregolya River Catchment, covering both the Polish and Russian parts, using the HYPE hydrological module and FyrisNP emission-retention model. The results revealed significant spatial variations in nutrient retention. The data assessment indicates that, at the start of the 21st century, the nutrient load from the Polish part of the catchment is significantly greater than that from the Russian part. Model simulations based on climatic projections for the years 2041–2060, but with current nutrient loads, showed a significant level of uncertainty in the changes of nutrient export to the Baltic Sea. The range for total nitrogen was –10 % to +27 %, and for total phosphorus it was –29 % to –10 %. Model simulations based on different socio-economic scenarios, but current climate conditions, showed that if present 5-year trends are maintained, nutrient export will only increase slightly (3 % for total nitrogen and total phosphorus). If the plans for socio-economic growth of Polish and Russian local governments are implemented, including the expansion of agriculture in Kaliningrad Oblast, there will be a significant increase in nutrient export (78 % for total nitrogen and 55 % for total phosphorus).