The lucrative fishing industry in the Great Australian Bight could be under threat if proposed oil drilling off Kangaroo Island goes ahead, said Flinders University Associate Professor in a report.

Flinders University Associate Professor Jochen Kaempf has raised concerns that nutrient-enriched seasonal upwellings in the area may be disrupted, potentially crippling South Australian fish stocks.

The up-flows are "the trigger of a highly productive marine food chain," Professor Kaempf said in his report.

"Environmentally and economically, we cannot risk this resource, without the nutrient rich water, the eastern Great Australian Bight would be a marine desert," he added.

The drilling sites approved by the federal government are within zones previously flagged as potential marine sanctuaries.