The impact of groundwater on pCO 2 variability was assessed in two coral reef lagoons with distinct drivers of submarine groundwater discharge (SGD). Diel variability of pCO 2 in the two ecosystems was explained by a combination of biological drivers and SGD inputs. In Rarotonga, a South Pacific volcanic island, 222 Rn-derived SGD was driven primarily by a steep terrestrial hydraulic gradient, and the water column was influenced by the high pCO 2 (5501 μatm) of the fresh groundwater. In Heron Island, a Great Barrier Reef coral cay, SGD was dominated by seawater recirculation through the sediments (i.e., tidal pumping), and pCO 2 was mainly impacted through the stimulation of biological processes. The Rarotonga water column had a higher average pCO 2 (549 μatm) . Over the course of this study, both systems were sources of CO 2 to the atmosphere with SGD-derived free-CO 2 most likely contributing a large portion to the air-sea CO 2 flux. Studies measuring the carbon chemistry of coral reefs (e.g., metabolism and calcification rates) may need to consider the effects of groundwater inputs on water column carbonate chemistry. Local drivers of coral reef carbonate chemistry such as SGD may offer more approachable management solutions to mitigating the effects of ocean acidification on coral reefs.