The Red Sea is characterized by its high seawater temperature and salinity, and the resilience of its coastal ecosystems to global warming is of growing interest. This high salinity and temperature might also render the Red Sea a favorable ecosystem for calcification and therefore resistant to ocean acidification. However, there is a lack of survey data on the CO2 system of Red Sea coastal ecosystems. A 1‐year survey of the CO2 system was performed in a seagrass lagoon, a mangrove forest, and a coral reef in the central Red Sea, including fortnight seawater sampling and high‐frequency pHT monitoring. In the coral reef, the CO2 system mean and variability over the measurement period are within the range of other world's reefs with pHT, dissolved inorganic carbon (DIC), total alkalinity (TA), pCO2, and Ωarag of 8.016±0.077, 2061±58 μmol/kg, 2415±34 μmol/kg, 461±39 μatm, and 3.9±0.4, respectively. Here, comparisons with an offshore site highlight dominance of calcification and photosynthesis in summer‐autumn, and dissolution and heterotrophy in winter‐spring. In the seagrass meadow, the pHT, DIC, TA, pCO2, and Ωarag were 8.00±0.09, 1986±68 μmol/kg, 2352±49 μmol/kg, 411±66 μatm, and 4.0±0.3, respectively. The seagrass meadow TA and DIC were consistently lower than offshore water. The mangrove forest showed the highest amplitudes of variation, with pHT, DIC, TA, pCO2, and Ωarag, were 7.95±0.26, 2069±132 μmol/kg, 2438±91 μmol/kg, 493±178 μatm, and 4.1±0.6, respectively. We highlight the need for more research on sources and sinks of DIC and TA in coastal ecosystems.