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regulated by intertidal vegetation such as cattails (freshwater) and cord grasses of the genus Spartina (salt water). The vegetation harbors many animal species and also protects a series of channels, which are hotspots for aquatic animal diversity and often nursery grounds for juveniles of many fish species. Tidal marshes often dominate the large number of coves, whose hydrodynamics and overall ecology are strongly affected by the enclosing peninsulas created by railroad construction in the nineteenth century. The marshes maybe sources of labile organic matter for the open Hudson River estuarine food web.

Shallow coves and bays are often covered by submarine attached vegetation, which includes at least twelve species, but is dominated by water celery. A number of coves have been successfully invaded by the floating water chestnut, a continuing source of annoyance to Hudson River residents. Despite this large amount of vegetation cover, most shallow areas consist of bare bottom and harbor a diverse benthic fauna (Chapter 19).

An extremely important but poorly understood habitat component of the Hudson River Estuary is the large suite of at least seventy-nine tributaries aside from the large Mohawk River, including rivers such as Indian Brook near Cold Spring and the Saw Mill River, which enters the river in Yonkers. The tributaries contribute approximately 20 percent of the water to the Hudson, a significant amount of particulate carbon and sedimentary material, and are crucial habitats for a wide variety of invertebrates and fishes. Alewifes use the tributaries extensively but we still do not know nearly enough about the importance of tributaries to the life cycles of a number of other fish species (Chapter 15). Interest in the Hudson's tributaries has heightened because urbanization has taken its toll on water quality and there is some evidence that the most urbanized tributaries contain greatly reduced fish populations.

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