In the late 1820′s, the Canterbury and Whitstable Railway Company built a railway from Canterbury to Whitstable and a new port at Whitstable to bring heavy goods such as coal from the north east. The railway between Canterbury and Whitstable, known as the Crab and Winkle line, was opened in 1830 and was the first in the world to carry passengers in trains drawn by steam power. The harbour was officially opened on the 19 March 1832, two years after the railway was finished. 10,000 people attended the opening, many coming by train from Canterbury in open wagons.
Although the harbour halved the cost of the transport of goods from London to north east Kent, the opening of the direct north Kent railway line, from London in 1861 proved competitive. The harbour continued, with the fishing industry doing well, and the introduction of new cargoes such as timber imports from the Baltic.
Road transport created more competition for the Crab and Winkle railway. The railway therefore closed to passenger traffic in 1932, freight continued with the harbour still open for coal, grain and timber.
When British Railways finally closed the railway line from Canterbury in 1952, the harbour lost much of its trade. The railway reopened briefly in 1953 when floods affected the main line, but closed permanently after that. In 1958 the Whitstable Urban District Council bought the harbour from the railway for £12,500.
In 1974 Whitstable Council became part of Canterbury City Council. The harbour is now managed by a Harbour Board, appointed by the council, which develops the harbour as a profitable mixed-use port for the benefit of the local community.