The world’s oceans contain an enormous reservoir of carbon, greater than either the terrestrial or atmospheric systems. The fluxes between these reservoirs are relatively rapid such that the oceans have taken up around 50% of the total carbon dioxide (CO2) released to the atmosphere via fossil fuel emissions and other human activities in the last 200 years. While this has slowed the progress of climate change, CO2 ultimately results in acidification of the marine environment. Ocean pH has already fallen and will continue to do so with certainty as the oceans take up more anthropogenic CO2. Acidification has only recently emerged as a serious issue and it has the potential to affect a wide range of marine biogeochemical and ecological processes. Based on theory and an emerging body of research, many of these effects may be non-linear and some potentially complex. Both positive and negative feedback mechanisms exist, making prediction of the consequences of changing CO2 levels difficult. Integrating the net effect of acidification on marine processes at regional and basin scales is an outstanding challenge that must be addressed via integrated programs of experimentation and modelling. Ocean acidification is another argument, alongside that of climate change, for the mitigation of anthropogenic CO2 emissions.