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The dock is L-shaped, with an 'Outer Dock' running east-west, and an 'Inner Dock' running north from the eastern end. It originally contained around 36 acres of water and had a 200 acre estate. The western end of the Outer Dock was originally connected to the Thames at Millwall by an 80 ft wide channel. The spoil from the docks formed the area of wasteland known as the Mudchute. A graving dock for ship repairs was constructed at the SE corner of the Outer Dock (one of 6 originally planned), and later lengthened to 555 ft.
With reorganisation by the Port of London Authority in the 1920s, the northern end of the Inner Dock was connected to the West India Docks by the Millwall Passage, and the direct connection to the Thames was filled.
The dock was used mainly for timber and grain, a trade which eventually moved down river to the Port of Tilbury with the construction of a major grain terminal in the 1960s. A McDougall's flour mill on the south side of the Outer Dock was demolished in about 1980.
A large site on the north side of Outer Dock is occupied by the West Ferry Printing Works, the largest newspaper print works in Western Europe, built 1984–6. Millwall Dock is a commercial business district that includes office towers housing small to medium sized technology, publishing, legal and financial services companies.
Millwall Dock lies near the centre of the Isle of Dogs, just south of the now developed Canary Wharf commercial business area. Millwall Dock is also an area where several housing developments and apartment towers have been developed. The Clippers Quay housing estate is located around the old dry dock, while the Mill Quay housing development is located on the site of the old flour mill. There is a marked contrast between the newly established living and working areas and the older neighbouring developments in the area.
Docklands Sailing and Water-sports Centre is located at the far West end of the dock where the dock previously connected to the Thames. It was set up in 1989 by the London Docklands Development Corporation and the Sports Council at a cost of £1.2 million.
The dock was a location for boat stunts in the 1999 James Bond film The World Is Not Enough.
There are three Docklands Light Railway stations serving the Millwall Dock, Mudchute, Crossharbour and South Quay.