There is a growing concern for how coral reefs may fare in a high-CO2 world. The majority of laboratory and mesocosm experiments have revealed negative effects on the growth and calcification of reef builders exposed to elevated CO2 conditions. However, coral reefs are highly dynamic systems and the interplay between different biogeochemical and physical processes on reefs results in large variability of seawater carbonate chemistry on different functional scales. This can create localized seawater conditions that can either enhance or alleviate the effects of ocean acidification (OA). Consequently, in order to predict how coral reef ecosystems may respond to OA in the future, it is necessary to first establish a baseline of natural carbonate chemistry conditions. This includes characterizing the range and variability of carbonate chemistry and the physical and biogeochemical controls across a broad range of environments over both space and time. Here, we have characterized the spatial and temporal physiochemical variability of two contrasting coral 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 research approaches including stationary autonomous sensors and spatial surveys during the month of November 2015. Mean and diurnal temporal variability in both physical and chemical seawater parameters were remarkably similar between sites and sampling depths, although, the magnitude of spatial variability was quite different between the sites. Spatial gradients in physiochemical parameters at Punta Caracol reflected the cumulative modification from terrestrial runoff and benthic metabolism. Based on graphical vector analysis of salinity normalized TA-DIC data, reef metabolism was dominated by organic carbon cycling over inorganic carbon cycling at both sites, where the outer reef reflected net heterotrophy likely owing to remineralization of organic matter from terrestrial inputs. Altogether, the results of this study highlight the strong influence of terrigenous runoff on reef metabolism and seawater chemistry conditions and demonstrate the importance of considering external inputs of alkalinity in reefs when interpreting TA-DIC data in systems with large freshwater inputs. Predicting future changes to coral reef ecosystems requires an understanding of the natural complexity of these systems in which various physical, ecological and biogeochemical drivers interact creating large variability in seawater chemistry over space and time.