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The Taunton River is one of the most intact ecosystems in New England and many of its habitats and species are ranked as global conservation targets. This unfragmented habitat from headwaters to the bay is regionally significant and hosts species found nowhere else in Massachusetts.

The ecosystems of the Taunton River are rich and varied. The corridor supports 31 distinct wildlife habitats and is inhabited by three globally rare plants. Rare natural communities include red maple and Atlantic white cedar swamps, which often contain vernal pools, criical habitat for rare reptiles and amphibians. Hessel's hairstreak, a globally rare butterfly, lives only in white cedar swamps. This watershed is also home to the water willow stem-borer moth, a species endemic to Southereastern Massachusetts' wetlands. This is the state's only species that is found nowhere else on earth.