In sharp contrast to the majority of temperate-zone lakes, where phosphorus is the nutrient that most limits primary productivity by algae and other aquatic plants and controls eutrophication, these processes are controlled by nitrogen inputs in most temperate-zone estuaries and coastal waters. This is largely because the natural flow of nitrogen into these waters and the rate of nitrogen fixation by planktonic organisms are relatively low while microbes in the sea floor sediments actively release nitrogen back to the atmosphere.

 When high nitrogen loading causes eutrophication in stratified waters — where a sharp temperature gradient prevents mixing of warm surface waters with colder bottom waters — the result can be anoxia (no oxygen) or hypoxia (low oxygen) in bottom waters. Both conditions appear to be becoming more prevalent in many estuaries and coastal seas. There is good evidence that since the 1950s or 1960s, anoxia has increased in the Baltic Sea, the Black Sea, and Chesapeake Bay. Periods of hypoxia have increased in Long Island Sound, the North Sea, and the Kattegat, resulting in significant losses of fish and shellfish.

 Eutrophication is also linked to losses of diversity, both in the sea floor community — including seaweeds, seagrasses, and corals — and among planktonic organisms. In eutrophied waters, for example, “nuisance algae” may come to dominate the phytoplankton community. Increases in troublesome or toxic algal blooms have been observed in many estuaries and coastal seas worldwide in recent decades. During the 1980s, toxic blooms of dinoflagellates and brown-tide organisms caused extensive die-offs of fish and shellfish in many estuaries. Although the causes are not completely understood, there is compelling evidence that nutrient enrichment of coastal waters is at least partly to blame for such blooms. 

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