In 1991 York Natural Environment Trust (YNET) was involved in a Public Planning Inquiry into a proposal by Persimmon Homes to develop land at Water Lane, Clifton, York. The group had first become involved in the land in 1989, when the York Green Site Survey run by Martin Hammond, which had been initiated by YNET, highlighted it as a valuable amenity and wildlife resource.

The Planning Inspector, after a week long Inquiry , overruled Persimmon's plans and after that negotiations began between Persimmon and Ryedale Council and a number of others involved to preserve a part of the site whilst permitting Persimmon to develop the rest. The product was what is known as a Section 106 agreement, which allocated an area of the site as a Nature Reserve, a section as a play area and also provided a commuted sum of money to be used in the management of the Nature Reserve.

The Section 106 agreement was signed in 1993 but it took until late 1997 when the site had moved in to the control of the new unitary authority, the City of York Council, that the work of the Clifton Backies Management Board actually began. This was commensurate with the work of the developers as outlined in the agreement.

Clifton Backies was officially designated a Local Nature Reserve in 2002, at which time the Friends of Clifton Backies group was formed.