The area was first settled by Saxons, from whom it takes its name (meaning literally [the place of] Wæppa’s people). It developed along the embankment of the Thames, hemmed in by the river to the south and the now-drained Wapping Marsh to the north. This gave it a peculiarly narrow and constricted shape, consisting of little more than the axis of Wapping High Street and some north-south side streets. John Stow, the 16th century historian, described it as a "continual street, or a filthy strait passage, with alleys of small tenements or cottages, built, inhabited by sailors’ victuallers".

Wapping was inhabited by sailors, mastmakers, boat-builders, blockmakers, instrument-makers, victuallers and representatives of all the other trades that supported the seafarer. Wapping was also the site of ’Execution Dock’, where pirates and other water-borne criminals faced execution by hanging from a gibbet constructed close to the low water mark. Their bodies would be left dangling until they had been submerged three times by the tide. Though Execution Dock is long gone, this gibbet is still maintained on the Thames foreshore by the Prospect of Whitby public house

Said to be England’s first, the Marine Police Force was formed in 1798 by magistrate Patrick Colquhoun and a Master Mariner, John Harriott, to tackle theft and looting from ships anchored in the Pool of London and the lower reaches of the river. Its base was (and remains) in Wapping High Street and it is now known as the Marine Support Unit. The Thames Police Museum, dedicated to the history of the Marine Police Force, is currently housed within the headquarters of the Marine Support Unit, and is open to the public by appointment.

In 1811, the horrific Ratcliff Highway murders took place nearby at The Highway and Wapping Lane.

The area’s strong maritime associations changed radically in the 19th century when the London Docks were built to the north and west of the High Street. Wapping’s population plummeted by nearly 60% during that century, with many houses destroyed by the construction of the docks and giant warehouses along the riverfront. Squeezed between the high walls of the docks and warehouses, the district became isolated from the rest of London, although some relief was provided by Brunel’s Thames Tunnel to Rotherhithe. The opening of Wapping tube station on the East London Line in 1869 provided a direct rail link to the rest of London.

Wapping was devastated by German bombing in World War II and by the post-war closure of the docks. It remained a run-down and derelict area into the 1980s, when the area was transferred to the management of the London Docklands Development Corporation, a government quango with the task of redeveloping the Docklands. The London Docks were largely filled in and redeveloped with a variety of commercial, light industrial and residential properties.

In 1986, Rupert Murdoch’s News International built a new £80m printing and publishing works in the north of Wapping. This became the scene of violent protests after News International’s UK operation moved from Fleet Street to Wapping, with over 5,000 print workers being sacked when new technology was introduced.

Perhaps Wapping’s greatest attraction is the Thames foreshore itself, and the venerable public houses that face onto it. A number of the old ’stairs’, such as Wapping Old Stairs and Pelican Stairs (by the Prospect of Whitby) give public access to a littoral zone (for the Thames is tidal at this point) littered with flotsam, jetsam and fragments of old dock installations. Understandably it is popular with amateur archaeologists and treasure hunters - it is surprisingly easy for even a casual visitor to pick up a centuries-old shard of pottery here.

Three venerable public houses are located near Stairs. By Pelican Stairs is the Prospect of Whitby, which has a much-disputed claim to be the oldest Thames-side public house still in existence. Be that as it may, there has been an inn on the site since the reign of Henry VIII, and it is certainly one of the most famous public houses in London. It is named after a then-famous collier that used to dock regularly at Wapping. A replica of the old Execution Dock gibbet is maintained on the adjacent foreshore, although the actual site of Execution Dock was nearer to the Town of Ramsgate. This also is on the site of a 16th-century inn and is located next to Wapping Old Stairs to the west of the Prospect; by Wapping Pier Head — the former local headquarters of the Customs and Excise.

Wapping has been used as the setting for a number of works of fiction, including The Long Good Friday; the Ruby In The Smoke novel in the Sally Lockhart series by Phillip Pullman and the brothel in The Threepenny Opera, in which Mack the Knife is betrayed by Jenny Diver.

Among the people born in Wapping are W.W. Jacobs, author of The Monkey’s Paw. The American painter James McNeill Whistler, well known for his Thames views, painted Wapping when he lived here between October 1860 and 1864. John Newton, Anglican clergyman and author of many hymns including Amazing Grace was born here. During the 1990s, Wapping was home to American entertainer Cher.