A diverse range of flora and fauna makes the island particularly interesting for naturalists.

Snake Island is part of the traditional territory of the Brataualung clan of the Gunai people, who named it "Negima".

Since the 1880s the island has been used by South Gippsland farmers to agist cattle in winter, swimming their stock over a narrow channel at low tide.

The vegetation communities of Snake Island include woodland, scrubland, heath, freshwater swamps, mangroves, and salt marsh.

Large numbers of migratory waders roost along the coast after feeding on the inlet's extensive intertidal mudflats.