The Exeter River Broad wetlands, forested riverbanks, and gently-flowing waters, interrupted by short stretches of rapids and falls, combine to make the Exeter River an important scenic resource as well as habitat for a variety of wildlife species in southeastern New Hampshire. As a major tributary to the Great Bay National Estuarine Reserve, the Exeter River also plays an vital role in maintaining the overall health of the bay's environment. For these reasons, the river has been recognized not only by the NH Rivers Management and Protection Program, but as part of the NH Resource Protection Project.
Great Bay is one of six high priority areas in the state recognized as a resource protection site.
A high level of water quality must be maintained in the Exeter River not only because of these designations, but because it is the primary source of municipal water supply for Exeter. The Exeter River begins in the town of Chester and flows east and north to Exeter where it becomes tidal and changes name to the Squamscott River, before emptying into Great Bay. Its drainage basin encompasses an area of 126 square miles. The upper 33.3 miles of the river, from its headwaters to its confluence with Great Brook in Exeter, were designated into the NH Rivers Management and Protection Program in August 1995. Land use along the Exeter River is primarily rural.