In the context of the European Water Framework Directive, we studied the possible impact of reduced emissions on phosphorus and nitrogen concentrations in a lowland river-lake system (Havel River, Germany). As a prerequisite, we quantified the retention of nutrients in the river from mass balances and deduced its seasonal variation. We detected that about 30% of the total nitrogen input is retained within the surveyed river section. In contrast, phosphorus release from sediments was shown to cause a considerable increase in present P concentrations. Average net phosphorus release rates of about 20 mg P m^−2 d^−1 in late summer were estimated for the Havel Lakes. Based on the observed patterns of N retention and P release we parametrized a newly developed water quality simulation program (TRAM), which allows alternative model approaches of different complexity to be implemented and tested. To account for the future trend of internal P loading, the phosphorus excess in lake sediments was estimated from core samples and included in the model as a state variable. For analyzing scenarios of reduced nutrient emissisions, the water quality simulation program was linked to mesoscale hydrological catchment models for the first time. From scenario simulations we conclude that internal P loading is likely to counteract efforts of emission control for decades. Even by significant reductions in external P loads, a persistent phosphorus limitation of primary production can hardly be established in the analyzed time frame of 13 years. Though in the short run a continued reduction in nitrogen loads appears to be the more promising approach of eutrophication management, we recommend enhanced efforts to diminish both N and P emissions.