The postgraduate aquaculture program develops an understanding of aquaculture principles and practices in a wide variety of fields. These include nutrition, water quality, reproduction, genetics, hatchery management, ecology, physiology, husbandry, production, health management, disease control, product quality, aquaculture systems, aquaculture technology, experimental design, statistics for biology, fisheries biology, management, and bio-business.

The courses draw on expertise from key industry figures in South Australia who serve on an industry consultative committee. Linked with these courses are work placements in tuna, yellowtail kingfish, oyster, abalone, mussel and freshwater crayfish sites. Flinders University is involved in research shared with Primary Industries and Resources South Australia (PIRSA) and the South Australian Research and Development Institute (SARDI).

The program involves practicals in laboratories, aquaria and tanks, aquaculture professionals and a flexible choice of elective topics available from different disciplines.