The Lakes and Coorong mulloway, cockle, yellow-eye mullet and golden perch fisheries officially began the assessment process Friday.
The fishery, which uses a wide range of gear types, includes the waters of the Coorong, Lake Alexandria, Lake Albert and some coastal waters near Kingston.
The main markets for the products are the domestic Australian markets.
MSC certification is being sought by the Southern Fisherman's Association and the World Wildlife Fund, and is expected to take eight to 10 months.
The certification will be carried out by Calif.-based Scientific Certification Systems.