This dataset contains high-frequency water temperature measurements collected on the outer reef slope (25 m) and central lagoon (12m) of Dongsha Atoll in the northern South China Sea. Temperature was recorded using Sea-Bird SBE56 thermistors mounted at fixed depths (25 m and 12 m). The instruments sampled at 1-minute intervals between 23 May 2017 and 27 October 2023 on the outer reef, and between 23 May 2018 and 28 Oct 2023 in the central lagoon, providing near continuous multi-year coverage of subsurface thermal conditions on a tropical coral reef. The measurements were collected to quantify fine-scale temporal variability in the reef-slope thermal environment, including diel to seasonal fluctuations, and to support research on physical processes influencing temperature dynamics on coral reef ecosystems. Data were obtained through autonomous in situ logging as part of a long-term observational programme aimed at characterising the thermal regimes of reefs influenced by oceanographic variability.