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 the most sensitive, animals. Moreover, to understand causes and effects, we need to identify the physiological processes sensitive to CO2 in animals. While the number of animals acutely sensitive to moderate CO2 increments may be small, long-term effects may have already begun in a wide range of species and these could drive shifts in ecological equilibria. Such effects not only include a disturbance in calcification. Recent studies of invertebrate fauna pre-adapted to oscillating CO2 levels in their habitat revealed a depression of metabolic rate associated with a reduction in ion exchange and protein synthesis rates as well as a shift in metabolic equilibria, resulting in a slowing of growth. Enhanced mortality has also been observed under long-term moderate hypercapnia with as yet unidentified cause and effect relationships. In a climate change scenario, simultaneous changes in temperature, CO2, and hypoxia levels would enhance sensitivity to environmental extremes relative to a change in only one of these variables. Some of these interactions are elicited through effects on the same physiological mechanisms, and need to be considered in estimating effects of atmospheric CO2 entry into the ocean. They also need to be considered in currently discussed mitigation scenarios such as direct injection of CO2 in the deep ocean or fertilizing the surface ocean with Fe, which reduces subsurface O2 contents. With changing CO2 levels, ecosystem shifts may develop progressively rather than beyond specific thresholds such that effects parallel CO2 oscillations. It is presently unclear, to what extent and how quickly species may adapt to permanently elevated CO2 levels by micro-evolutionary compensatory processes.