Aquatic animals are diverse in terms of species, but also in terms of production systems, the people involved, and the benefits achieved. In this concept piece, we draw on literature to outline how the diversity of aquatic animals, their production, and their consumption all influence their impact within the food system. Built on evidence from an array of reductionist and non-reductionist literature, we suggest that food systems researchers and policymakers adapt current methods and theoretical frameworks to appropriately contextualise aquatic animals in broader food systems. We do this through combining current understandings of food systems theory, value chain, livelihoods, nutritional outcomes, and planetary boundaries thinking. We make several claims around understanding the role of aquatic animals in terms of nutritional output and environmental impacts. We suggest a need to consider: (1) the diversity of species and production methods; (2) variable definitions of an “edible yield”; (3) circular economy principles and the impacts of co-products, and effects beyond nutrient provision; (4) role of aquatic animals in the overall diet; (5) contextual effects of preservation, preparation, cooking, and consumer choices; (6) globalised nature of aquatic animal trade across the value chain; and (7) that aquatic animals are produced from a continuum, rather than a dichotomy, of aquaculture or fisheries. We conclude by proposing a new framework that involves cohesive interdisciplinary discussions around aquatic animal foods and their role in the broader food system.