Understanding the contributions of diffuse and point sources to nitrate pollution is crucial for managing river water quality. We conducted a long-term modeling study for the Rhine and Elbe basins and their 146 subbasins from 1950 to 2021 to quantify the roles of diffuse and, in particular, point sources in driving stream NO_₃–N concentrations. In both basins, simulated results show a decline in point source contributions from 1950 to 2000, followed by a relatively stable level at around 25% in the Rhine and fluctuations around 30% levels in the Elbe. The decline in the simulated stream NO_₃–N concentrations in both basins after 1990 was largely driven by a decrease in point sources, and stream NO_₃–N concentrations remained high (∼2 mg l⁻¹) during 2010–2021, even when point sources were excluded. At the subbasin level, changes in point source contributions and stream NO_₃–N concentrations reflected the overall trends of their respective basins, although individual subbasins exhibited diverse patterns. In subbasins with high stream NO_₃–N concentrations during 2010–2021, point source contribution accounted for around 30% (median values across subbasins), and the fractions of agricultural, urban, and industrial land cover were relatively high. These results highlight that point source management alone is not sufficient to reduce stream nitrate to a good ecological status (< 2 mg l⁻¹), and spatial targeted management is required to achieve good ecological status at both the regional and local levels.