Currently rising CO2 levels in atmosphere and marine surface waters as well as projected scenarios of CO2 disposal in the ocean emphasize that CO2 sensitivities need to be investigated in aquatic organisms, especially in animals which may well be the most sensitive. Moreover, to understand causes and effects, we need to identify the physiological processes that are sensitive to CO2 beyond the current emphasis on calcification. Few animals may be acutely sensitive to moderate CO2 increases, but subtle changes due to long-term exposure may already have started to be felt in a wide range of species. CO2 effects identified in invertebrate fauna from habitats characterized by oscillating CO2 levels include depressed metabolic rates and reduced ion exchange and protein synthesis rates. These result in shifts in metabolic equilibria and slowed growth. Long-term moderate hypercapnia has been observed to produce enhanced mortality with as yet unidentified cause and effect relationships. During future climate change, simultaneous shifts in temperature, CO2, and hypoxia levels will enhance sensitivity to environmental extremes relative to a change in just one of these variables. Some interactions between these variables result from joint effects on the same physiological mechanisms. Such interactions need to be considered in terms of future increases in atmospheric CO2 and its uptake by the ocean as well as in terms of currently proposed mitigation scenarios. These include purposeful injection of CO2 in the deep ocean or Fe fertilization of the surface ocean, which reduces subsurface O2 levels. The resulting ecosystem shifts could develop progressively, rather than beyond specific thresholds, such that effects parallel CO2 oscillations. It is unsure to what extent and how quickly species may adapt to permanently elevated CO2 levels by microevolutionary compensatory processes.