The Brataualung clan of the Kurnai (Gunai) people occupied the area of Waratah Bay and Cape Liptrap for over 6000 years. Axes and other stone tools were made from quartzite and jasper gathered from Cape Liptrap, chipped to a sharp edge and ground with sandstone. Middens containing charcoal, stone flints and the remains of shellfish mark the location of camps along the coast. The Superb Fairy-wren was the totem of the Brataualung clan. The male birds were known as "dedyung" and the females as "neryung". They are common throughout the park today.
 
The small township and bustling port of Waratah (now Walkerville) operated from 1875 to 1926 to supply lime to the Melbourne building industry. Limestone mined from the cliffs was burnt with firewood in brick lined-kilns (resembling up-turned bottles) to produce quick lime. The lime was then bagged and hauled in tram carts along a 350 metre jetty which once stretched out into the bay to waiting ships.

Relics of the lime industry remain in the park including the ruins of the kilns in the cliffs at Walkerville South and the formation of tramways which were once used for hauling firewood to the kilns.

A lighthouse was established at Cape Liptrap in 1913 to improve the safety of coastal shipping. In 1951 the steel tower was dismantled and replaced with the current structure. The light is still in operation and has a range of 18 nautical miles (over 34 kilometres).