Water temperature data in and around Dongsha Atoll (Taiwan), northern South China Sea. The dataset spans from 2013 to 2016, with temporal coverage varying among the 20 sampling sites. The data are stored in a MATLAB structure; including temperature in °C, time in UTC (i.e. GMT) in MATLAB date format, latitude, longitude, and water depth of the sensor. All data were collected with Onset Corp. HOBO U22 temperature loggers, which were all calibrated in an isothermal bath before deployment to an accuracy of 0.1 °C. The temperature loggers were deployed on subsurface floats, typically ~1 meter above the bed.