The Domesday Survey recorded eight mills in this area, and as windmills came later, these must have been tidal water mills on the River Lea and so they are among the earliest known tide mills in England. In medieval times the site was known as Three Mills. They provided flour for the bakers of Stratford-atte-Bow, who supplied bread to the City of London. In 1588, one of the two remaining mills was described as a gunpowder mill.

In 1728, Three Mills was bought by Peter Lefevre, a Huguenot, who entered into partnership with Daniel Bisson and several others. The mills operated in conjunction with a distillery and the company had its own carpenters, coopers and operated a large piggery fed on waste products. They also continued to mill for other purposes including supply to the Royal Navy Victualling Office.

Built on an existing pre-Domesday site it is a timber framed building clad in brick on three sides. In addition to flour making, the mill served the famous distillery next door on Three Mills Island. Built across the River Lea, the Mill trapped the sea and river water at high tide to turn the water wheels on the ebb. The outflowing water turned four large wheels driving twelve pairs of millstones. These four wheels and six of the pairs of millstones survive together with other historic machinery. The Mill ceased milling in 1941 after the area was bombed during the Second World War.

The House Mill was built in 1776 by Daniel Bisson, on the site of an earlier mill and between two houses occupied by the miller and his family, hence its name. The Clock Mill opposite was rebuilt in 1817. There was also a third mill, a windmill, which survived until about 1840. The House Mill continued to operate until 1941 and the Clock Mill until 1952.