Shadwell was originally a parish liberty associated with the parish of Stepney, but became a separate parish in its own right in 1670. In 1889 it was transferred from Middlesex to the newly-created County of London and in 1900 became part of Stepney Metropolitan Borough. Stepney Metropolitan Borough was abolished in 1965, and became part of the London Borough of Tower Hamlets in Greater London.
In the 13th century, the area was known as Scadflet and Shatfliet – derived from the Anglo-Saxon fleot, meaning a shallow creek or bay – the land was a low lying marsh, until drained (by order of Act of Parliament, after 1587) by Cornelius Vanderdelf. A spring, issuing from near the south wall of the churchyard was dedicated to St Chad, and filled a nearby well. The origin of the name is therefore confused, being associated with both the earlier use and the later well. Shadwell was formerly called Chadwelle.
In the 17th century, Thomas Neale became a local landowner, and built a mill and established a waterworks on large ponds, left by the draining of the marsh. The area had been virtually uninhabited and he developed the waterfront, with houses behind as a speculation. Shadwell became a maritime hamlet with roperies, tanneries, breweries, wharves, smiths, and numerous taverns, built around the chapel of St Paul's. Seventy-five sea captains are buried in its churchyard; Captain James Cook had his son baptised there.
The modern area is dominated by the enclosed former dock, Shadwell Basin, whose construction destroyed much of the earlier settlement – by this time degenerated into slums. The basin once formed the eastern entrance to the then London Docks, with a channel leading west to St Katharine Docks. It is actually two dock basins - the south basin was constructed in 1828-32 and the north basin in 1854-8.
Unlike nearby Limehouse Basin, few craft larger than canoes can be seen on Shadwell Basin, which is largely used for fishing and watersports - and as a scenic backdrop to the modern residential developments that line it. The basin, however, is still connected to the Thames and the channel is spanned by a bascule bridge.
In the 19th century, Shadwell was home to a large community of foreign South Asian lascar seamen, brought over from British India by the East India Company. There were also Anglo-Indians, from intermarriage and cohabitation between lascar seamen and local girls. There were also smaller communities of Chinese and Greek seamen, who also intermarried and cohabited with locals.
St. Paul's Shadwell with St. James Ratcliffe, is traditionally known as the Church of Sea Captains. In 1656 the church was established as a Chapel of Ease, from St Dunstan's, at Stepney. In 1669, it was rebuilt as the Parish Church of Shadwell, and it was the last of five parish churches rebuilt after the Restoration. In 1820, it was again rebuilt as a 'Waterloo church'.
Captain James Cook was an active parishioner and John Wesley preached in the church from time to time. Isham Randolph of Dungeness, one of Thomas Jefferson's grandfathers and son of William Randolph, was married in St. Paul's church. Father of Thomas Jefferson, Peter Jefferson and whose father Thomas Jefferson had and built his estate in Ablemarle County, Virginia's boyhood home was named Shadwell after the Shadwell parish.