Globally, estuaries are considered important CO2 sources to the atmosphere. However, estuarine water carbonate chemistry and CO2 flux studies have focused on temperate and high latitude regions, leaving a significant data gap in subtropical estuaries. In this study, we examined water column carbonate system and air–water CO2 flux in the Mission-Aransas Estuary, a subtropical semiarid estuary in the northwestern Gulf of Mexico, by collecting samples at five System Wide Monitoring Program stations from 05/2014 to 04/2015. The carbonate system parameters (total alkalinity [TA], dissolved inorganic carbon [DIC], pH, CO2 partial pressure [pCO2], and carbonate saturation state with respect to aragonite [XAr]) and air–water CO2 flux all displayed substantial seasonal and spatial variations. Based on freshwater inflow conditions, a drought period occurred between 05/2014 and 02/2015, while a flooding period occurred from 03/2015 to 04/2015. Average DIC was 2194.7 6 156.8 lmol kg21 and 2132.5 6 256.8 lmol kg21 , TA was 2497.6 6 172.1 lmolkg21 and 2333.4 6 283.1 lmol kg21 , pCO2 was 477 6 94 latm and 529 6 251 latm, and CO2 flux was 28.3 6 18.0 mmol Cm22 d21 and 51.6 6 83.9 mmolCm22 d21 in the drought and flooding period, respectively. Integrated annual air–water CO2 flux during our studied period was estimated to be 12.4 6 3.3 molCm22 yr21, indicating that this estuary was a net CO2 source. High wind speed, warm climate, riverine input, and estuarine biogeochemical processes all contributed to the high CO2 efflux despite the modest pCO2 levels year round.