Indonesia is the world's second largest producer and third largest consumer of seafood. Fish is therefore essential to the nation, both financially and nutritionally. Overfishing and the effects of climate change will, however, limit future landings of capture fisheries, so any increases in future seafood production will need to come from aquaculture. The ecological effects of aquaculture are dependent upon the choice of species, management, and where it is sited. In the present study we use life cycle assessment (LCA) to evaluate how possible interventions and innovations can mitigate environmental impacts related to the aquaculture sector's growth. The mitigation potential of six interventions were also quantified, namely (1) FCR reductions for whiteleg shrimp, carp, and tilapia; (2) sustainable intensification of milkfish and Asian tiger shrimp polyculture; (3) shifting groupers from whole fish diets to pellets; (4) favoring freshwater finfish over shrimp; (5) renewable electricity; and (6) reduced food waste and improved byproduct utilization. If all six interventions are implemented, we demonstrate that global warming, acidification, eutrophication, land occupation, freshwater use, and fossil energy use could be reduced by between 28% and 49% per unit of fish. The addition of many innovations that could not be quantified in the present study, including innovative feed ingredients, suggest that production could double within the current environmental footprint. This does not, however, satisfy the expected 3.25-fold increase under a business-as-usual scenario, neither does it satisfy the government's growth targets. We therefore also explore possible geographical areas across Indonesia where aquaculture expansions and ecological hotspots may conflict. Conclusively, we advocate more conservative production targets and investment in more sustainable farming practices. To accelerate the implementation of these improvements, it will be central to identify the most cost-effective aquaculture interventions.