West India Quay station is located over the northern half of the dock of the same name in southeast end of Limehouse and is very close to both Poplar and Canary Wharf, and is in the central portion of the London Borough of Tower Hamlets.

Situated to the south of Billingsgate Road and Aspen Way (A1261), the station is near the edge of the main Docklands re-development area.

[9] Between March and October 2007 the station's canopy was replaced in a £1.85m project funded by Transport for London.

The new track goes around West India Quay, before coming back up to rejoin the route to Canary Wharf.

After reconstruction, the old platform 1 ceased to exist with trains from Westferry diving under the junction and bypassing the station to the east.