Aquaculture, fueled partly by claims of supporting food security, is experiencing unprecedented growth. Framing aquaculture as a monolith, however, overlooks its extreme taxonomic diversity. This paper assesses the welfare risks associated with that diversity, establishing seven species-level risk factors from involved parental care to long lifespans. Investigating these welfare risks across all aquatic species reported to the Food and Agriculture Organization (FAO) revealed an uneven distribution of risk, with extreme species-level risks in chordates, crustaceans, and cephalopod mollusks. Compared to species with fewer risks, species with extreme welfare risks were found to cost more and contribute the least to global production. This work challenges the notion that prioritizing animal welfare is incompatible with addressing food security and creates the possibility of identifying certain plant and invertebrate species, like seaweeds and bivalves, that minimize welfare concerns while providing affordability and accessibility. Going forward, proactive welfare approaches are needed to inform consumer choice and shape just and sustainable aquaculture policy.