Ocean acidification alters fish populations indirectly through habitat modification

Ocean ecosystems are predicted to lose biodiversity and productivity from increasing ocean acidification1. Although laboratory experiments reveal negative effects of acidification on the behaviour and performance of species2, 3, more comprehensive predictions have been hampered by a lack of in situ studies that incorporate the complexity of interactions between species and their environment. We studied CO2 vents from both Northern and Southern hemispheres, using such natural laboratories4 to investigate the effect of ocean acidification on plant–animal associations embedded within all their natural complexity. Although we substantiate simple direct effects of reduced predator-avoidance behaviour by fishes, as observed in laboratory experiments, we here show that this negative effect is naturally dampened when fish reside in shelter-rich habitats. Importantly, elevated CO2 drove strong increases in the abundance of some fish species through major habitat shifts, associated increases in resources such as habitat and prey availability, and reduced predator abundances. The indirect effects of acidification via resource and predator alterations may have far-reaching consequences for population abundances, and its study provides a framework for a more comprehensive understanding of increasing CO2 emissions as a driver of ecological change