Exponentially rising CO₂ (currently ~400 µatm) is driving climate change and causing acidification of both marine and freshwater environments. CO₂ directly affects acid–base and ion regulation, respiratory function and aerobic performance in aquatic animals. Elevated CO₂ projected for end of this century (e.g. 800–1000 µatm) can also impact physiology, and have substantial effects on behaviours linked to sensory stimuli (smell, hearing and vision) both having negative implications for fitness and survival. In contrast, the aquaculture industry was farming aquatic animals at CO₂ levels that far exceed end-of-century climate change projections (sometimes >10 000 µatm) with limited detrimental effects reported. Potential explanations for this discrepancy include 1) the use of ‘control’ CO₂ levels in aquaculture studies that go beyond 2100 projections in an ocean acidification context; 2) the relatively benign environment in aquaculture (abundant food, disease protection, absence of predators) compared to the wild; 3) aquaculture species having been chosen due to their natural tolerance to the intensive conditions, including CO₂ levels; or 4) the breeding of species within intensive aquaculture having further selected traits that confer tolerance to elevated CO₂. We highlight this issue and outline the insights that climate change and aquaculture science can offer for both marine and freshwater settings. Integrating these two fields will stimulate discussion on the direction of future cross-disciplinary research. In doing so, this article aimed to optimize future research efforts and elucidate effective mitigation strategies for managing the negative impacts of elevated CO₂ on future aquatic ecosystems and the sustainability of fish and shellfish aquaculture.