The most significant process degrading the Black Sea has been the massive over-fertilization of the sea by compounds of nitrogen and phosphorus, largely as a result of agricultural, domestic and industrial sources. This over-fertilization produces a phenomenon called eutrophication that has changed the structure of the Black Sea ecosystem. The nitrogen and phosphorus compounds (nutrients) enter the Black Sea from sources from the 17 countries in its drainage basin, particularly through rivers. It is estimated that the six Black Sea countries contribute about 70% of the total amount of the substances flowing to the Black Sea as waste from human activities. Some of this amount and almost all of the remaining 30% (from the other eleven non-coastal countries) enter the Sea via the Danube River.

In the 1970s and 1980s, the Black Sea ecosystem suddenly collapsed. Vast amounts of dead plants and animals covered the beaches of Romania and western Ukraine, and between 1973 and 1990, losses were estimated as 60 million tons of bottom animals including 5 million tons of fish. The catastrophe was a consequence of eutrophication – the over-enrichment of water bodies with organic matter which results in lack of oxygen and severe reductions in water quality and in fish and other animal populations. The effects of eutrophication were felt across the entire Black Sea.

The most important source of organic matter in the sea are floating plants – phytoplankton species – that grow in all surface waters where there is enough light and essential nutrients, particularly the nitrogen and phosphorus compounds upon which all plant life depends. In the sea, different plant species bloom when the conditions for them are right, and later fade to be replaced by other species in much the same way as flowers and grasses in a meadow. They are often grazed, eaten by marine animals known as zooplankton. These in turn are consumed by larger animals in a food chain which often ends with fish or mammals such as dolphins, seal and humans. Almost all animals in the sea share a common requirement for oxygen. Enough oxygen dissolves in seawater to sustain marine animals, except for mammals and some reptiles, which come to the sea's surface for air.

The North-western part of the Black Sea is largely below one hundred meters deep and always received a good supply of nutrients from the rivers Danube and Dnipro, Europe's second and third largest rivers. It was virtually covered with underwater meadows. The meadow, was the home to a unique and highly productive ecosystem of plants and animals. The ecosystem, however, rather suddenly and catastrophically collapsed starting in the 1970s. Discharges of waste nutrients from agricultural activities, and from domestic and industrial sources across the Black Sea basin, entered rivers and streams and eventually found their way to the Black Sea itself. The seagrass and algal beds of the north-western shelf were unable to absorb such large amounts of nutrients and large quantities of phytoplankton began to grow, shading the light from the larger plants below. Deprived of light, the meadows began to die.

The effects of eutrophication were felt across the entire Black Sea. Though it is estimated that 70% of the dissolved nutrients produced by human activity came from the Danube River alone, all countries contributed and coastal eutrophication is observed in areas well away from the influence of the Danube. Indeed, the whole sea suffered changes in the structures of its ecosystem during the last three decades and eutrophication is one of the factors that have contributed to this change. (Based on: L. Mee, "How to save the Black Sea, Your Guide to the Black Sea Strategic Action Plan", 2000).

What contributed to the waters pollution in the Black Sea and Danube Basin region was, for example, the discharge of insufficiently treated sewage. Such discharges constitute a threat to public health and in some cases pose a barrier to the development of sustainable tourism and aquaculture. Black Sea ecosystem is also affected by oil pollution, radioactive substances, and solid waste. Toxic substances such as pesticides and heavy metals do not appear to pollute the entire Black Sea but form "hot spots" near well-identified sources. Hot spots - the main points discharging high levels of pollution loads originating from domestic or industrial sources –on the coast of the Black Sea affect human health, ecosystems, sustainability or economy. 49 hot spots have been identified in the region, including 9 in Bulgaria, 6 in Georgia, 6 in Romania, 8 in Russia, 10 in Turkey and 10 in Ukraine. The possible transboundary effects of hot spots may involve: fisheries, resulting in a decline in productive capacity; destruction of wetlands and habitat of migratory fauna; biodiversity, by endangering some species located in the region; landscape, by reducing the regional value of Black Sea tourism; accidents polluting transboundary zones; and public health.