The aim of this study is to produce future scenarios on the river inputs of water and nutrients (nitrate and phosphate) into the Mediterranean and Black Sea. They are based on the four contrasting scenarios that were developed by the Millenium Ecosystem Assessment (MEA) for the years 2030 and 2050 and implemented in a spatially explicit manner into the IMAGE model. We first identified the major drivers of the river fluxes by regression analyses, then tested the retained models against the past evolutions between 1970 and 2000, and finally applied the models to the MEA scenarios. For nutrients, the considered river data mainly refer to the large rivers for which long-term time series exist (Rhone, Po, Ebro, and Danube). Here, recent trends were principally driven by fertilizer spreads (NO3, PO4), together with urban wastewater releases (PO4). Future trends remain in the envelope of the observed variability during the last 40 years, both for the large rivers and, when extrapolated to the basin scales, also for the entire Mediterranean and Black Sea. At regional scales, however, the budgets considerably change. In the northern parts of the Mediterranean drainage basin, they uniformly tend to decrease, but they may strongly increase in the south and east. Water discharge is examined on a basis of 37 rivers, showing that this parameter is clearly linked to the evolution of climate. Because of the ongoing evolution toward dryer and warmer conditions, we predict a significant trend of decreasing freshwater fluxes for the future, which already started in the past. Regional hot spots for this decrease are the drainage basin of the Alboran Sea and, when also considering the inhabitant specific water fluxes, the basins of the Aegean and north Levantine seas.