Rivers are important sources of freshwater and nutrients for the Mediterranean and Black Sea. We present a reconstruction of the spatial and temporal variability of these inputs since the early 1960s, based on a review of available data on water discharge, nutrient concentrations and climatic parameters. Our compilation indicates that Mediterranean rivers suffer from a significant reduction in freshwater discharge, contrary to rivers of the Black Sea, which do not have clear discharge trends. We estimate this reduction to be at least about 20% between 1960 and 2000. It mainly reflects recent climate change, and dam construction may have reduced discharge even further. A similar decrease can also be expected for the fluxes of dissolved silica (Si), strongly controlled by water discharge and potentially reduced by river damming as well. This contrasts with the fluxes of nitrogen (N) and phosphorus (P) in Mediterranean and Black Sea rivers, which were strongly enhanced by anthropogenic sources. Their total inputs to the Mediterranean Sea could have increased by a factor of >5. While N still remained at elevated levels in 2000, P only increased up to the 1980–1990s, and then rapidly dropped down to about the initial values of the 1960s. With respect to the marine primary production that can be supported by the riverine nutrient inputs, Mediterranean and the Black Sea rivers were mostly phosphorus limited during the study period. Their anthropogenic nutrient enrichment could only have had a fertilizing effect before the general decline of the P loads. When also considering Si as a limiting element, which is the case for siliceous primary producers such as diatoms, silica limitation may have become a widespread phenomenon in the Mediterranean rivers since the early 1980s. For the Black Sea rivers, this already started the late 1960s. Gross primary production sustained by rivers (PPR) represents only less than 2% of the gross production (PP) in the Mediterranean, and less than 5% in the Black Sea. Possible ecological impacts of the changing river inputs should therefore be visible only in productive coastal areas, such as the Gulf of Lions, where PPR can reach more than two thirds of PP. Reported ecosystem changes both in the Adriatic Sea and the Black Sea are concomitant with major changes in the reconstructed river inputs. Further work combining modelling and data collection is needed to test whether this may also have been the case for coastal ecosystems at other places in the Mediterranean and Black Sea.