Identifying the long-term effects of ocean acidification (OA) and global warming on coral calcification has proven elusive yet has major implications for the continuing viability of coral reefs in the face of climate change. Here we address this question using seasonally and annually resolved boron proxies (11B/10B and B/Ca) of calcifying fluid (cf) pHcf and carbonate ion concentrations ([CO3 2−]cf) preserved in a long-lived Porites coral from the Great Barrier Reef (GBR). From 1939 to 2013 we find that the coral pHcf closely followed the decline in seawater pH of ∼0.1 units, but at a reduced rate of ∼60%, indicative of biological buffering. Of the decline in pHcf ∼82% is attributed to OA and ∼17% to the ∼0.5 °C long-term warming observed over this period. This long-term warming induced change in pHcf is consistent with the much larger seasonally modulated changes in pHcf where ∼4 to 6 °C seasonal changes in temperatures are accompanied by relatively large antithetic ∼0.1 changes in pHcf. Furthermore, we find that although the supply of dissolved inorganic carbon (DIC) of the coral cf has remained at constant elevated levels of ∼1.5 × seawater, there has been a significant long-term decline (4 to 11%) in the [CO3 2−]cf, due primarily to the OA-induced change in pHcf. This decline in [CO3 2−]cf, a critical parameter controlling calcification, is thus likely responsible for the ∼15% decline in coral calcification observed since 1939 and across the GBR generally.