The fort was built between 1808 and 1812 to prevent invaders gaining access from Maidstone Road to the River Medway. The work was composed of a long brick revetted dry ditch running between a fortified guardroom on the Rochester-Maidstone Road to a similar tower alongside the Medway. The principal work is a massive red brick keep, in the style of a medieval castle, which served as gun tower and observation post. In the sides of the tower were embrasures to sweep the ditch with fire. The dry ditch running across St Margaret's Street was crossed by drawbridge through a substantial casemated guardhouse in the form of an arch . From the tower ran a series of tunnels to the outlying guardhouses. Behind the dry ditch running from the tower down to Maidstone Road was a range of domestic building and barracks.
After 1815, the fort served a variety of purposes, including military prison and lunatic asylum. After nearby Fort Pitt became a military hospital, the patients were moved from Clarence to a new asylum, although the prison remained, with accounts of floggings being given in local newspapers. The fort was used by the garrison artillery throughout the First World War as a recruiting centre. After the war, a large Territorial and Volunteer Reserve centre was built alongside the site and the main barrack site run down. During the Second World War, the Home Guard used Fort Clarence as headquarters and, with the invasion scare, the fort was pressed into service again.
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