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Coral reef community composition and ecosystem function may change in response to anthropogenic ocean acidification. However, the magnitude of acidification on reefs will be modified by natural spatial and temporal variability in seawater CO2 chemistry. Consequently, it is necessary to quantify the ecological, biogeochemical, and physical drivers of this natural variability before making robust predictions of future acidification on reefs. In this study, we measured temporal and spatial physiochemical variability on a reef flat in Kane'ohe Bay, O'ahu, Hawai'i, using autonomous sensors at sites with contrasting benthic communities and by sampling surface seawater CO2 chemistry across the reef flat at different times of the day during June and November. Mean and diurnal temporal variability of seawater CO2 chemistry was more strongly influenced by depth gradients (0.5-10 m) on the reef rather than benthic community composition. Spatial CO2 chemistry gradients across the reef flat reflected the cumulative influence from benthic metabolism, bathymetry, and hydrodynamics. Based on graphical assessment of total alkalinity-dissolved inorganic carbon data, reef metabolism in November was dominated by organic carbon cycling over inorganic carbon cycling, while these processes were closely balanced in June. Overall, this study highlights the strong influence of depth on reef seawater CO2 chemistry variability through its effects on benthic biomass to seawater volume ratio, seawater flow rates, and residence time. Thus, the natural complexity of ecosystems where a combination of ecological and physical factors influence reef chemistry must be considered when predicting ecosystem biogeochemical responses to future anthropogenic changes in seawater CO2 chemistry.