Submarine groundwater discharge (SGD) flows into coral reefs. In volcanically active areas; the incoming groundwater is typically CO2-rich which can alter the carbon balance and views on how coral reefs function at prevailing high CO2. We quantified dynamic hydrothermal SGD and CO2 fluxes to a Philippine coral reef over a spring-neap tidal cycle. SGD rates; with mean of 35 cm d−1 and 5−95% range of 0−147.8 cm d−1 . The groundwater-CO2 fluxes (266 mmol m d−1; range: 0−1111 mmol m2 d−1) were up to ∼300-fold larger than evasion of CO2 to the atmosphere. The reef seawater pCO2 (493 μatm; range: 421−680 μatm) remained above atmospheric values and spanned the upper end of the range of atmospheric levels (400−500 μatm) expected for the next century. Because of the hydrothermal SGD; the reef has prevailing above-atmospheric CO2 and is a source to the atmosphere and nearby waters.