The island has been subject to diamond exploration following the discovery of a wide range of kimberlite indicator minerals there, which was continuing as of 2019[update].

[citation needed] The Flinders Island Whaling and Sealing Site is listed on the South Australian Heritage Register.

[7] Some time prior to 1911, sheep, horses, cattle, milk thistles and oats were introduced to Flinders Island, presumably by Willie Schlink and his family.

[11][12] An account of Flinders Island's wildlife published in 1934 stated that penguins could "be seen waddling soldier-like among the rocks and cave entrances that constitute their homes".

[13] In 2006 there was an colony of little penguins believed to be "probably declining", with an estimated population of fewer than twenty birds, nesting at the base of some cliffs where feral cats have limited access.

[14] A risk assessment for the penguins commissioned by Department for Environment & Natural Resources in 2016 report based their recommendations on the 2006 estimate.

[9] In early 2025 Federal Government funding was increased to A$3.8 million, with the aim of eradicating feral cats, black rats and mice by the end of 2025, with reintroductions of native species to take place one year after the island is declared as being pest-free.

[20] The island has been subject to diamond exploration following the discovery of a wide range of kimberlite indicator minerals there,[21] which was continuing as of 2019[update].