Global warming and ocean acidification are driving gradual declines in seawater dissolved oxygen concentrations and pH. Predicting how these changes will affect shallow, near-shore environments including coral reefs is challenging due to high natural variability on both spatial (10 m to km) and temporal (diel to seasonal) scales. To make predictions, it is first necessary to identify and quantify the drivers of this natural variability. While significant efforts have been devoted to characterising the influence from metabolic processes on coral reef seawater chemistry, less attention has been devoted to physical processes such as flow speed and light intensity. Here, we measured seawater flow, photosynthetically active radiation (PAR), pH, and dissolved oxygen (DO) at three reef habitats (reef flat, lagoon, and outflow channel) in a fringing coral reef system in Okinawa, Japan for a duration of 3 weeks in October of 2019. During the study, circulation was primarily wave-driven with mean flow speeds ranging from 14-26 cm/s. Flow direction became increasingly consistent at higher flow speeds, which traced visual patterns in the benthos observed from 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 35-69% of the observed variability. The results demonstrate that flow speed, trajectory, and PAR play important and variable roles in controlling biogeochemical variability within coral reefs and need to be considered in assessing their vulnerability to global climate change.

This dataset was collected in Onna-son, Okinawa, Japan (26.449720°N, 127.794245°E), over three weeks in October 2019. pH, temperature, oxygen and salinity data from C1 were collected with a SeapHOx. pH was recoreded at C2 and C3 by SeaFETs, while temperature and salinity were recorded at these sites by Seabird SBE 16 plus V2 SeaCAT recorder equipped with oxygen optodes (Aanderaa Oxygen Sensor 3835). Drifter experiments were conducted using Pacific Gyre reef drifters with their position recorded every minute via iridium telemetry. Flow speed, direction and pressure were measured at C1 using a Nortek Vector ADV, at C2 & C6 by Nortek 2 MHz Aquadopps, and at C3, C7, and C8 by Nortek 1 MHz Aquadopps, and at C4 and C5 by 1 MHz Teledyne Sentinels. Pressure was measured at P1 and P2 by RBR Virtuosos. Photosynthetically active radiation was recorded at C1 by an ECO-photosynthetically active radiation (PAR) sensor from Wetlabs, Seabird Scientific. Data were processed using MATLAB.

Instrument locations are in the attached .mat file. A key to each variable has also been uploaded.