The museum opened in 2003 in grade I listed early 19th-century Georgian "low" sugar warehouses built in 1802 on the north side of West India Docks, a short walk from Canary Wharf.

[3] The periods covered range from the first port on the Thames in Roman times to the closure of the central London docks in the 1970s and the subsequent transformation of the area with commercial and residential developments.

[5][6] London Museum Docklands has a lecture theatre and meeting rooms and hosts talks and events connected with the docks.

[7][8] By the 2010s the museum had decided to rationalise its collection of vessels; one was transferred to a local group, and another, the Wey barge Perseverance IV, to the National Trust.

[13] In September of that year, the museum displayed Dick Moore's George Cross medal for bravery during the London Blitz.