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There is growing concern about the effects of ocean acidification (OA) on coral reefs, with many studies indicating decreasing calcium carbonate production and reef growth. However, to accurately predict how coral reefs will respond to OA, it is necessary to characterize natural carbonate chemistry conditions, including the spatiotemporal mean and variability and the physical and biogeochemical drivers across different environments. In this study, spatial and temporal physiochemical variability was characterized at two contrasting reef locations in Bocas del Toro, Panama, that differed in their benthic community composition, reef morphology, and exposure to open ocean conditions, using a combination of approaches including autonomous sensors and spatial surveys during November 2015. Mean and diurnal temporal variability in both physical and chemical seawater parameters were similar between sites and sampling depths, but with occasional differences in extreme values. The magnitude of spatial variability was different between the two sites, which reflected the cumulative effect from terrestrial runoff and benthic metabolism. Based on graphical vector analysis of TA–DIC data, reef metabolism was dominated by organic over inorganic carbon cycling at both sites, with net heterotrophy and net calcium carbonate dissolution dominating the majority of observations. The results also highlight the potentially strong influence of terrestrial freshwater runoff on surface seawater conditions, and the challenges associated with evaluating and characterizing this influence on benthic habitats. The Bocas del Toro reef is a unique system that deserves attention to better understand the mechanisms that allow corals and coral reefs to persist under increasingly challenging environmental conditions.