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Human impact

Of the thirty-two largest cities in the world in the early 1990s, twenty-two were located on estuaries.

As ecosystems, estuaries are under threat from human activities such as pollution and overfishing. They are also threatened by sewage, coastal settlement, land clearance and much more. Estuaries are affected by events far upstream, and concentrate materials such as pollutants and sediments. Land run-off and industrial, agricultural, and domestic waste enter rivers and are discharged into estuaries. Contaminants can be introduced which do not disintegrate rapidly in the marine environment, such as plastics, pesticides, furans, dioxins, phenols and heavy metals.

Such toxins can accumulate in the tissues of many species of aquatic life in a process called bioaccumulation. They also accumulate in benthic environments, such as estuaries and bay muds: a geological record of human activities of the last century. The elemental composition of biofilm reflect areas of the estuary impacted by human activities, and over time may shift the basic composition of the ecosystem, and the reversible or irreversible changes in the abiotic and biotic parts of the systems from the bottom up.

For example, Chinese and Russian industrial pollution, such as phenols and heavy metals, has devastated fish stocks in the Amur River and damaged its estuary soil.

Estuaries tend to be naturally eutrophic because land runoff discharges nutrients into estuaries. With human activities, land run-off also now includes the many chemicals used as fertilizers in agriculture as well as waste from livestock and humans. Excess oxygen-depleting chemicals in the water can lead to hypoxia and the creation of dead zones. This can result in reductions in water quality, fish, and other animal populations.Overfishing also occurs. Chesapeake Bay once had a flourishing oyster population that has been almost wiped out by overfishing. Oysters filter these pollutants, and either eat them or shape them into small packets that are deposited on the bottom where they are harmless. Historically the oysters filtered the estuary's entire water volume of excess nutrients every three or four days. Today that process takes almost a year, and sediment, nutrients, and algae can cause problems in local waters.

Some major rivers that run through deserts historically had vast, expansive estuaries that have been reduced to a fraction of their former size, because of dams and diversions. One example is the Colorado River Delta in Mexico, historically covered with marshlands and forests, but now essentially a salt flat.