AbstractGroundwater inputs are typically overlooked as drivers of environmental change in coastal reef studies. To assess the impact of groundwater discharge on reef biogeochemistry, we examined two fringing reef environments, located in Maunalua Bay on the south shore of O‘ahu, Hawai‘i, that receive large inputs of submarine groundwater discharge. We supplemented 25‐ and 30‐d time series measurements of salinity, water temperature, pH, dissolved oxygen, and 222Rn with high‐resolution 24‐h nutrient, dissolved inorganic carbon (DIC), total alkalinity (TA), and δ13C–DIC measurements to evaluate both groundwater‐induced and biologically‐driven changes in coastal carbonate chemistry across salinity gradients. Submarine groundwater discharge at these two locations was characterized by low pHT (7.36–7.62), and variable DIC (1734–3046 μM) and TA (1716–2958 μM) content relative to ambient seawater. Groundwater‐driven variability in coastal carbonate system parameters was generally on the same order of magnitude as biologically‐driven variability in carbonate system parameters at our study locations. Further, our data revealed a shift in reef metabolism from net dissolution to net calcification across this groundwater‐driven physicochemical gradient. At sites with high levels of groundwater exposure, net community production and calcification rates were reduced. Our findings shed light on the importance of considering groundwater inputs when examining coastal carbonate chemistry.