Central to evaluating the effects of ocean acidification (OA) on coral reefs is understanding how calcification is affected by the dissolution of CO2 in sea water, which causes declines in carbonate ion concentration [CO32-] and increases in bicarbonate ion concentration [HCO3-]. To address this topic, we manipulated [CO32-] and [HCO3-] to test the effects on calcification of the coral Porites rus and the alga Hydrolithon onkodes, measured from the start to the end of a 15-day incubation, as well as in the day and night. [CO32-] played a significant role in light and dark calcification of P. rus, whereas [HCO3-] mainly affected calcification in the light. Both [CO32-] and [HCO3-] had a significant effect on the calcification of H. onkodes, but the strongest relationship was found with [CO32-]. Our results show that the negative effect of declining [CO32-] on the calcification of corals and algae can be partly mitigated by the use of HCO3- for calcification and perhaps photosynthesis. These results add empirical support to two conceptual models that can form a template for further research to account for the calcification response of corals and crustose coralline algae to OA.