Rapid climate change in the Northeast Atlantic and Arctic poses a threat to some of the world’s largest fish populations. Impacts of warming and acidification may become accessible through mechanism-based risk assessments and projections of future habitat suitability. We show that ocean acidification causes a narrowing of embryonic thermal ranges, which identifies the suitability of spawning habitats as a critical life-history bottleneck for two abundant cod species. Embryonic tolerance ranges linked to climate simulations reveal that ever-increasing CO2 emissions [Representative Concentration Pathway (RCP) 8.5] will deteriorate suitability of present spawning habitat for both Atlantic cod (Gadus morhua) and Polar cod (Boreogadus saida) by 2100. Moderate warming (RCP4.5) may avert dangerous climate impacts on Atlantic cod but still leaves few spawning areas for the more vulnerable Polar cod, which also loses the benefits of an ice-covered ocean. Emissions following RCP2.6, however, support largely unchanged habitat suitability for both species, suggesting that risks are minimized if warming is held “below 2°C, if not 1.5°C,” as pledged by the Paris Agreement.