There is considerable evidence that Corner Inlet has been an important part of human experiences for over 5,000 years with Aboriginal shell middens being plentiful along the southern shore. The Brataolong clan of the Gunai/Kurnai tribe has strong cultural traditions and practices associated with the Corner Inlet area. Many Aboriginal sites including scarred trees, burial sites, artefact scatters, camps and shell middens have been recorded in the area.

Europeans settled in the area in the mid 1800s and established various mining, agricultural and forestry enterprises. Fishing became established by the 1860s once regular steamers made their way from the region back to Melbourne.

Changes in the catchment for Corner Inlet have been significant with much of the area which collects freshwater that enters the Inlet now being cleared from the forests which once covered South Gippsland. With these changes much greater volumes of sediment flowed into Corner Inlet, one possible cause for the disappearance of many of the Poisidonia seagrass beds in the northern section of the Inlet.