Unlike Norfolk and Phillip Islands, Nepean is not volcanic in origin, but is Late Pleistocene limestone formed from wind blown sand dunes between the last two ice ages.

Calcareous sand grains were bound by carbonate cement to form a calcarenite limestone.

[1] It is thought the island was named in 1788 by Lieutenant Philip Gidley King for Evan Nepean, Under-Secretary of State for the Home Department, who was involved with arrangements for the dispatch of the First Fleet and with administration of the colony of New South Wales during its early years.

[3][1] The island is made of calcareous rock dating from the late Pleistocene and is a breeding site for several species of seabirds.

It is a refuge for the endemic marbled gecko, which is now extinct on Norfolk Island.