Aquatic foods are a critical source of human nutrition in many developing countries. As a result, declines in wild-caught fish landings threaten nutritionally vulnerable populations. Aquaculture presents an opportunity to meet local demand, but it also places pressure on natural resource inputs and causes a range of environmental impacts. Here, we examine whether current aquaculture systems in Bangladesh can be reoriented to address prevailing nutritional deficiencies while minimizing these environmental impacts. Current fish farming practices, even when optimized, cannot fully supply the same essential micronutrient densities of zinc, iron and calcium as wild-caught fish. However, when the proportion of highly nutrient-dense small indigenous fish species (SIS) was increased to at least 30% of the total output in any of the 14 aquaculture production systems analysed, these systems were able to meet or surpass the nutrient densities of average wild-capture fisheries. Extensive aquaculture systems that co-produce fish and rice had the lowest environmental burdens in six out of seven metrics examined when the composition of all aquaculture systems was modified to include 50% SIS. Nutrition-sensitive aquaculture that provides greater human health benefits and minimizes environmental impacts is a key societal challenge that requires targeted interventions and supportive policies.