The main cause of the increasing eutrophication in the sea is nutrient inputs from the rivers. The catchment area of the Black Sea is over 2 million square kilometers, five times the size of the sea itself. The drainage basin entirely or partially covers 22 countries in Europe and Asia Minor. The largest volume of river flow entering the sea comes from the north-western part of the basin. Depending on meteorological, hydrothermal, and hydrobiological conditions during summer and autumn, oxygen deficiency (hypoxia or anoxia) and mass mortality caused by eutrophication have become an annual event in the north-western shelf area where anoxic zones expanded from covering 3 500 square kilometers in 1973 to 40 000 square kilometers in 1990. This level of eutrophication also puts the 13 % of water volume of the shelf area that is not anoxic under severe stress. 

Oil spills cause serious deterioration of the coastal marine ecosystem through contamination of water and sediment, aesthetics quality, etc. Some 170 thousand tones of oil products are discharged into the Black Sea every year with sewage. Pollutants and toxic agents are also carried to the sea in river waters. The highest concentrations of hydrocarbons (petroleum residuals) were detected in the Danube, Dnieper and Dniester river estuaries and other point sources of pollution located off the shores of Romania and Bulgaria where oil production and refining is carried out. The Danube River accounts for 48 % of the 111 000 tones of oil entering the Black Sea via rivers each year. In addition, ports, oil terminals and their immediate surroundings, and straits are at risk from maritime accidents involving ships transporting crude oil. In Sevastopol Bay, the major port for the Black Sea navy, oil concentrations more than 100 times higher than background level were measured. 

Large-scale construction of cascade dams on the Dnieper and Don and other rivers has led to the loss of spawning areas for the sturgeon and other valuable fish species due to their being cut off from the sea. Moreover the drastic decrease of annual river flow has resulted in apparent hydro-chemical and biochemical changes, with catastrophic effects in the low salinity basins. Significant damage to the productivity of sea areas is also caused by the intake of cooling water by various installations along the coast. Despite the fact that about 80 % of these have fish protection devices at their water intake, their efficiency remains rather low and several thousands tones of fish die each year. Implementation of a new technology to control the quality of coastal waters and increase biodiversity, the construction of artificial reefs, began in the 1970s. At present, special constructions have been built in Constanța port (Romania) and Odessa Bay (Ukraine). 

Over-exploitation has affected fish stocks. Commercial fishing in the Dnieper and Dniester estuaries has been reduced. Some valuable species such as mackerel, bonito and horse mackerel in the Black Sea and pike, perch, roach and bream in the Sea of Azov have practically disappeared. Of the 26 commercial fish species found in the period 1960 to 1970, only five were left by 1980. By the mid-1980s, sturgeon catches had nearly reached the average annual amount for the 1930s of 1 000 tones, but farm-produced fish accounting for more than 90 % of the total catch. Commercial mussel farming is practiced in all countries except Georgia and Turkey. Importation of species for aquaculture has induced severe alterations at the ecosystem level.