Well before the arrival of European settlers, the Agawam established semi-permanent agricultural villages here, harvesting shellfish in and around the islands in the warmer months. During the 18th and 19th centuries, Choate Island and Long Island, connected by a causeway, comprised a prosperous farming community. The c.1778 Proctor Barn on Long Island and the c.1725–40 Choate family homestead stand as reminders of this agricultural past.
The Refuge was established in 1974, with endowment, by bequest, in 1991, as a gift of Miné S. Crane in memory of her husband, Cornelius Crane; both are buried at the summit of Choate Island. Additional land was given by Mr. and Mrs. Walter A. Swan in 1981, Robert S. Hardy and Ann R. Hardy in 1993; Beatrice Woodbury in 1995; and Janet Hopkins in 1995. The purchase of Pine Island occurred in 2000, and gift of additional marshland came from Keddah Trust in 2001.