Most of the land in the Stony Brook Valley Preserve was acquired for the Museum by John Hay, the eminent natural history writer and principal founder and benefactor of the organization, and other public-spirited citizens. To ensure this land is forever preserved, the Trustees of the Museum gave a conservation restriction on the land to the Brewster Conservation Trust.

The Museum retains ownership and the right to use the land for education, passive recreation, and scientific research. The two organizations work together to maintain trails for the public; to protect wild areas from human intrusion and invasive species; and to consider joint projects in environmental education, research, habitat enhancement, and public programming.

A grant received from the New England Natural Areas and Wildlife Grant Program helped support a project to enhance habitat for both common and uncommon bird species, including migrating birds that use the land for breeding, feeding, and shelter. Sensitive stewardship helps protect these critical habitats for state-listed threatened and special concern species, and maintains a landscape of historic and scenic importance. As noted in a study prepared for CCMNH by Michael Lach from The Compact of Cape Cod Conservation Trusts and the Harwich Conservation Trust, the land is within the Old King's Highway Regional Historic District, which encompasses an area where the earliest colonial settlements existed on Cape Cod.

The herring run probably attracted Native Americans like the Wampanoag to the area long before the colonists arrived, and a lost Factory Village, the major industrial center of Brewster in the 18th and 19th centuries, was located at the head of the stream at Stony Brook Road.