A recent expert review of the ecological risks of net pen aquaculture in the North American Great Lakes made a number of recommendations for Best Management Practices (BMPs) that should be applied to establishment of net pen farms. Based on that_study, researchers identified nine generic BMPs that could be applied to all Global Great Lakes. These were: adopt adaptive management (AM), apply before-after-control- impact (BACI) to assess new farms under AM, siting must insure adequate flushing and good quality water while avoiding sensitive environments, culture native and endemic species, maintain biosecurity protocols to reduce risk of disease occurrence and transmission, vigorously pursue all available practices to minimize net-pen effluents, develop management plan for wild fishes within/near boundaries of net pen farm, limit entry of new farms to the assimilation capacity of the whole lake, and require plan and bond for decommissioning. Researchers then reviewed the first commercial net pen farm on the African Great Lakes (in Lake Malawi) to determine if these BMPs were implemented, and how well they performed in constraining ecological risks. Eight of the nine BMPs were applied to some degree and immediate risks were minimal. However, some of the issues arising around allocation of wild fish attracted to the farm site were contentious. The major challenge of developing the net pen aquaculture industry and applying the BMP is the setting of lake-wide water quality targets for lake nutrient concentrations and nutrient loading, and will require cooperative action and agreement by riparian nations.