The data are one year (summer 2016 - summer 2017) of continuous pH (seafet), Salinity, and temperature measurements in a seagrass, coral reef and mangrove ecosystem of the Red Sea. Monthly statistics of pH, Salinity and Temperature are also provided for the three ecosystems. Full characterization of the carbonate system was done every 15 days on discrete samples from measurement of dissolved inorganic carbon and total alkalinity. In a subset of samples, the pH was also measured spectrophotometrically to compare with the pH from the Seafet sensors.At the coral reef site, the SeaFET mooring started the 16.06.2016 and was interrupted the 09.05.2017 because of sensor malfunction, with three interruptions for maintenance, between the 31.08.2016 and the 30.09.2016, the 11 and the 18.11.2016 and the 27 and the 30.03.2017. The CTD moorings were conducted in parallel to the SeaFET moorings. At the seagrass site, a malfunction of the CTD caused a gap of data between the 12.11.2016 and the 20.01.2017, two more interruptions for maintenance occurred between the 03 and the 09.03.2017 and between the 11 and the 20.06.2017. At the coral reef site, two interruptions for maintenance occurred between the 05 and the 17.11.2017 and between the 03 and the 09.06.2017.