The aim of the modeling studies (MONERIS) was to estimate annual source apportioned nitrogen (N) and phosphorus (P) emissions into the Vistula and Oder basins in 1995-2008, thus, during the transition period in Poland, characterized by changes in both agricultural sector and handling of point source pollution. N and P emissions into both basins showed declining tendencies. Between the sub-periods 1995-2002 and 2003-2008, the overall N emission into the Vistula and Oder basins decreased by 16-17% (i.e. by ca. 26,900 tons in the Vistula and by ca. 18,000 tons in the Oder basin); P emission declined by 23% in the Vistula and by 32% in the Oder basins (i.e. by ca. 3400 tons in the Vistula and by ca. 2200 tons in the Oder basin). The temporal patterns of N and P emission into the Vistula and Oder basins, as well as the percentage contribution of N and P pathways (particularly: overland flow, tile drainage, groundwater, waste water treatment plants) showed great differences between the basins. Natural (type of bedrock, soil type, lake area) and anthropogenic (regionally and temporarily different type and intensity of agricultural activity, spatially different structural changes in agriculture during the transition period, regionally and temporarily different investment in waste water treatment plans) factors were found to be responsible for the differences, and the relationships are extensively discussed in the paper. In 1995-2008, 70% of N emission into both river basins was via groundwater and tile drainage, with the former playing more important role in the Vistula basin, and the latter playing more important role in the Oder basin; contribution of N emission from point sources was comparable in both rivers and it reached 11-12%. In 1995-2008, point sources, erosion, overland flow, and urban systems were found the most important P pathways in both basins, with a higher percentage contribution of point sources in the Oder basin.