Waquoit Bay holds deep cultural and ecological significance for the Upper Cape region. The Mashpee Wampanoag Tribe has lived in this area for over 12,000 years—the name Waquoit is derived from the Wampanoag word Weeqayut, meaning “Place of Light.” Over time, the bay has supported a range of livelihoods, including milling, cranberry farming, tourism, and both commercial and subsistence fisheries for species like herring, quahogs, and oysters.

The Waquoit Bay watershed is home to the Mashpee National Wildlife Refuge—a 6,000-acre conservation area spanning the towns of Falmouth and Mashpee. This refuge encompasses a rich mosaic of aquatic habitats, from coastal estuaries and freshwater rivers to wetlands, ponds, and rare Atlantic white cedar swamps. Its upland landscapes include meadows, forests, and pine barrens, contributing to the area's remarkable biodiversity.

Three major river systems flow into Waquoit Bay: Red Brook, and the Quashnet and Childs rivers. All were historically altered to accommodate cranberry farming, leaving lasting impacts on streamflow and habitat. Today, the lower sections of the Quashnet and Childs rivers have been fully restored and now support self-sustaining populations of sea-run Brook Trout and other native species. However, the upper reaches of the Quashnet River and Red Brook—along with adjacent abandoned cranberry bogs—remain in need of restoration to fully reconnect and revitalize these critical coldwater systems.

While many of the bay’s tributaries are being brought back to life, Waquoit Bay itself faces growing threats. Excess nutrients from residential septic systems and fertilizer runoff have degraded water quality, contributing to fish and shellfish die-offs and the decline of vital eelgrass beds—nurseries for countless marine species. These issues are not unique to Waquoit Bay. Without a comprehensive approach to wastewater management, estuaries across Cape Cod will continue to decline.