The area now occupied by the museum formed part of Low Hall Farm, purchased from the Bosanquet family by Walthamstow Urban District Council in 1875. Since the 14th century, the 200-acre site had been home to a moated country house, Low Hall Manor, which subsequently gave its name to the farm. The council acquired the land in order to build a sewage pumping station.
Despite the considerable antiquity of the site, nothing now remains above ground of the medieval manor house, nor of the 17th century building that succeeded it. Both were completely destroyed by a V1 'flying bomb' in 1944. In 1997 the Museum of London Archaeology Service excavated the site and a number of interesting artefacts were found.