Rivers contribute significantly to the pollution and eutrophication that have caused drastic changes to the ecosystem of the Black Sea1-3. Although damming is known to affect riverborne nutrient loads, and thus riverine ecosystems, evidence for significant effects in open coastal waters is sparse4-6. Here we present long-term data sets of water and nutrient discharge from the River Danube to the Black Sea. These data reveal a reduction in the dissolved silicate load of the river by about two-thirds since dam constructions in the early 1970s. A concomitant decrease in wintertime dissolved silicate concentrations by more than 60% was observed in central Black Sea surface waters. The consequent changes in silicon to nitrogen ratio of the Black Sea nutrient load appear to be larger than those caused by eutrophication alone, and seem to be responsible for dramatic shifts in phytoplankton species composition from diatoms (siliceous) to coccolithophores and flagellates (non-siliceous). Our results strongly suggest that the damming of the Danube has been instrumental in causing the observed changes in Black Sea surface waters3,7-9, and that the large number of dams in operation around the world today could similarly affect the food web structure and biogeochemical cycling in coastal seas.