It was named in 1802 after the British politician and colonial administrator Sir Evan Nepean by John Murray in HMS Lady Nelson.
The point includes Cheviot Beach on its southern side, notable as the site of the disappearance in 1967 of Australia's then-Prime Minister Harold Holt.
[5] The area's early settlers mined limestone from the coastal cliffs, and two lime kilns were built around 1840.
It contains the oldest buildings erected for quarantine purposes in Australia, four of the main hospital buildings (established in 1857), pre-dating the oldest intact quarantine-related structures at North Head, Sydney, by 16 years.
[citation needed] Australia's first major oil spill occurred off Point Nepean in 1903, with the wreck of SS Petriana.
In 2004, 90 hectares (220 acres) of Defence land was transferred to the Commonwealth government's Point Nepean Community Trust, which managed the former Quarantine Station until the land was transferred to the Victorian government on 8 June 2009.
Some of the historic features include (major features shown in bold): The coast of Point Nepean contains intertidal reef platforms with high invertebrate diversity as well as subtidal reefs with diverse communities of fish, invertebrates and encrusting organisms such as ascidians, sponges Dale and bryozoans.