Defining sustainability goals is a crucial but difficult task because it often involves the quantification of multiple interrelated and sometimes conflicting components. This complexity may be exacerbated by climate change, which will increase environmental vulnerability in aquaculture and potentially compromise the ability to meet the needs of a growing human population. Here, we developed an approach to inform sustainable aquaculture by quantifying spatio-temporal shifts in critical trade-offs between environmental costs and benefits using the time to reach the commercial size as a possible proxy of economic implications of aquaculture under climate change. Our results indicate that optimizing aquaculture practices by minimizing impact (this study considers as impact a benthic carbon deposition ≥ 1 g C m-2  day-1 ) will become increasingly difficult under climate change. Moreover, an increasing temperature will produce a poleward shift in sustainability trade-offs. These findings suggest that future sustainable management strategies and plans will need to account for the effects of climate change across scales. Overall, our results highlight the importance of integrating environmental factors in order to sustainably manage critical natural resources under shifting climatic conditions.