The maritime history of Cockatoo Island began within a decade of the penal settlement being established. As the volume of shipping in Port Jackson increased, Governor Gipps proposed to his Imperial masters in London the construction of a dry dock for the repair of Royal Navy and other vessels. Work started in 1847 with gunpowder blasting the rock and convicts manually excavating the site. It took ten years to construct Fitzroy Dock, a considerable time but convicts had little incentive to break their backs in the service of authorities.

The Sutherland Dock was built between 1882 and 1890, and for a short time was the largest single graving dock in the world. Shipbuilding began in 1870 and by World War I over 150 dredges, barges and tugs had been built. Slipways were later built south of the Fitzroy Dock and the island’s biggest slipway, Slipway Number 1, was constructed in the Northern Shipyard in 1912. Most of the early shipbuilding activity took place on the slipways located to the east of the Engineers' and Blacksmiths' Shop on the Eastern Apron. Cockatoo Island became the Naval Dockyard of the Royal Australian Navy in 1913.

As World War II approached the tempo of activity increased and continued for the duration of the war. Merchant ships and luxury liners were converted to troop transports, stores and hospital ships. Post-war shipbuilding continued at pace, including notably the Daring Battle Class Destroyers HMAS Voyager and HMAS Vampire. In 1962, Cockatoo Island won the tender to construct Empress of Australia, which when completed in 1965, was the largest roll-on roll-off cargo passenger ship in the world. In 1979 the contract was signed for the construction of the last ship to be built at Cockatoo Island. HMAS Success was the largest naval vessel built in Australia and may still be seen in Sydney Harbour from time to time.