This data set documents carbonate chemistry data for the seawater and prorewater samples collected from the seagrass meadows in the inner lagoon (IL) and on the northern shore (NS) of Dongsha Island, as well as the total carbon content (TC), total nitrogen content (TN), median grain size, and water content for the sediment cores collected on the NS and southern shore (SS), and in the IL of Dongsha Island. Table 1 lists the sampling locations; Table 2 shows the median grain size, water content, TC, and TN data in the sediment cores collected from the NS, SS, and IL sites; Table 3 shows seasonal diel pH, dissolved inorganic carbon (DIC), total alkalinity (TA) and partial pressure of CO2 (pCO2) data in the seagrass meadows of the IL and NS sites; and Table 4 shows pH, DIC, TA, pCO2, saturation state of aragonite (a) and Ca2+ data in the porewater of the sediment cores collected at the NS, SS, and IL sites.