AbstractGlobal warming and ocean acidification are driving declines in seawater dissolved oxygen (DO) concentrations and pH. Predicting how these changes will affect shallow, near‐shore environments such as coral reefs is challenging due to their high natural biogeochemical variability present over both spatial (m to km) and temporal (diel to seasonal) scales. To make predictions, we must understand the drivers of this variability. The impact of metabolic processes on coral reef biogeochemical variability has been the subject of significant research effort, however, physical factors, including flow speed and light intensity, have received less attention. Here, we measured seawater flow, photosynthetically active radiation (PAR), pH, and DO at three reef habitats (reef flat, lagoon, and outflow channel) in a fringing coral reef system in Okinawa, Japan for 3 weeks in October 2019. During the study, pH ranged from 7.86 to 8.37 units while DO varied from 127 to 369 μmol/kg. Circulation was primarily wave‐driven with mean flow speeds ranging from 14 to 26 cm/s. Flow direction became increasingly consistent at higher flow speeds and traced benthic striations visible in satellite imagery. Multiple linear regression models of daytime changes in pH and DO versus daily mean flow speed and PAR described 25%–74% of the observed variability across all sites while at night, flow speed alone accounted for 7%–75% of the observed variability. These results demonstrate PAR, water flow speed, and the path water takes play important roles in controlling biogeochemical variability within coral reefs and must be considered when assessing their vulnerability to both local and global environmental change.