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The Taunton River is the longest undammed coastal river in New England and provides excellent habitat for all life stages of fish. The estuary is particularly valued for its nursery habitat for fish such as winter flounder and tautog, as well as for its large anadromous fish runs, particularly river herring.

Currently, dams limit or eliminate access to spawning habitats on some tributaries, but there is huge potential for restoration of species such as herring, shad, and rainbow smelt through selective dam removal. Coldwater fishery habitats are also present on some Taunton River tributaries, providing rare habitat niches in this low gradient watershed. Other important fisheries habitats include riffles, oxbows, fresh and salt water marshes, and native aquatic vegetation beds. The Taunton River supports about 45 species of fish and many species of shellfish.