Technical Abstract: An increased demand has pushed extensive aquaculture towards intensively operated production systems, commonly resulting in eutrophic conditions and cyanobacterial blooms. This review summarizes cyanobacterial secondary metabolites that can cause undesirable tastes and odors (odorous metabolites) or are biochemically active (bioactive metabolites) in marine and freshwater, extensive and intensive aquaculture. For the scope of this paper, biochemically active metabolites include (1) toxins that can cause mortality in aquaculture organisms or have the potential to harm consumers via accumulation in the product (hepatotoxins, cytotoxins, neurotoxins, dermatoxins, and brine shrimp/molluskal toxins), (2) metabolites that may degrade the nutritional status of aquaculture species (inhibitors of proteases and grazer deterrents) or (3) metabolites that have the potential to negatively affect the health of aquaculture species or aquaculture laborers (dermatoxins, irritant toxins, hepatoxins, cytotoxins). Suggestions are made as to future management practices in intensive and extensive aquaculture and the potential exposure pathways to aquaculture species and human consumers are identified.