Whitstable harbour was built in 1832 by the Canterbury and Whitstable railway company in order to serve the "Crab and Winkle" line, the world's first passengerrailway service. The Crab and Winkle line also carried coal, and linked Canterbury and London via a steam ship from Whitstable harbour.

By 1849, the town was reported in the local press as "Prospering rapidly thanks to the harbour and railways." During the second world war, the harbour was used to transport munitions and grain, and sustained very little damage, however, it fell into disrepair, and was only kept alive by a group of local people after the closing of the Crab and Winkle line in 1952.

After a town referendum, the Whitstable Urban District Council bought the harbour and repairs began. By 1963, the first R.N.L.I crew was recruited from local harbour users, and their presence is still highly valued today. In 1947, the harbour came under the administration of Canterbury City Council, and now covers fourteen acres, with three quays. About 150 local people are employed by the harbour, where fishing, fish processing, coal and timber transport are still the main business activities.

The harbour fish markets are popular with locals and visitors alike, and a restaurant is also situated in the harbour, ready to serve up the day's catch. In the summer months, visitors flock to the stalls which spring up to delight their customers with all manner of fresh sea food, including the famous Whitstable oysters.