Poland, with its large drainage area, with 50% contribution of agricultural land and 45% contribution of population to overall agricultural land area and population number in the Baltic catchment, is the largest exporter of riverine nitrogen (N) and phosphorus (P) to the sea. The economic transition has resulted in substantial, statistically significant decline in N, P export from Polish territory to the Baltic Sea. Following the obligations arising from the Helsinki Commission (HELCOM) declarations, in the coming years, Poland is expected to reduce riverine N loads by ca. 25% and P loads by ca. 60% as referred to the average flow normalized loads recorded in 1997–2003. The aim of this paper is to estimate annual source apportioned N and P emissions into these river basins in 2015 and 2020 with application of modeling studies (MONERIS). Twelve scenarios, encompassing changes in anthropogenic (diffuse, point source) and natural pressure (precipitation, water outflow due to climate change), have been applied. Modeling outcome for the period 2003–2008 served as our reference material. In applied scenarios, N emission into the Oder basin in 2015 and 2020 shows an increase from 4.2% up to 9.1% as compared with the reference period. N emission into the Vistula basin is more variable and shows an increase by max. 17.8% or a decrease by max. 4.7%, depending on the scenario. The difference between N emission into the Oder and Vistula basins is related to the catchment peculiarities and handling of point sources emission. P emission into both basins shows identical scenario patters and a maximum decrease reaches 17.8% in the Oder and 16.7% in the Vistula basin. Despite a declining tendency in P loads in both rivers in all the scenarios, HELCOM targeted P load reduction is not feasible.