Tropical estuarine deltas generally present poorly buffered waters in their freshwaters. Carbonate chemistry predicts that mixture of such warm freshwater with seawater will create rapid consumption of the freshwater carbon dioxide (CO2) by the carbonate buffering capacity of the seawater. In this study, we used the Paraiba do Sul River as a laboratory to investigate how thermodynamics compare with biological processes, gas exchange, and tidal advection from mangrove. We conducted three spatial surveys covering the salinity gradient of the main channel and surrounding mangrove waters and one 24-h mooring in a mangrove creek. In the main channel, dissolved inorganic carbon (DIC) and total alkalinity (TA) showed closely conservative distribution along the salinity gradient, increasing seaward. The partial pressure of CO2 (pCO2) followed a bell-shaped curve predicted by carbonate chemistry for conservative mixing of river and ocean endmembers. During high river flow, pCO2 sharply decreased between salinities 0 and 5 (1800 to 390 ppmv), a pCO2 drawdown attributed to riverine outgassing and thermodynamics. Indeed, the mixing of TA-poor freshwater (363 ± 16 μmol kg−1) with TA-rich seawater creates a deficit of dissolved CO2 not related to biotic processes. During low river flow, the entire mixing zone was undersaturated in pCO2 with an increasing trend seaward. However, observed pCO2 values were slightly above those predicted by conservativity. Approximately half of this deviation was attributed to biological activity (net heterotrophy), and remaining deviation was assigned to the effects of gas exchange (18%) and water heating (36%). The effect of gas exchange was higher in fresh and low salinity waters, reflecting the higher outgassing/ingassing of CO2, and lower buffering capacity. Water heating was more important in mid- to high-salinities as a result of diel patterns of solar irradiance. Heterotrophy was slight and not able to outcompete thermodynamics and generate outgassing during estuarine mixing. Consistently, stable isotopic signatures of DIC (δ13C-DIC) presented slight deviations below the conservative mixing, corroborating net heterotrophy in the main channel. Areas of CO2 uptake due to phytoplankton activity were identified but restricted to the freshwater endmember during low river flow, with lowest pCO2 (up to 41 ppmv) and the highest chlorophyll a (up to 21.3 μg L−1). The estuary was a CO2 sink during low river flow (−1.34 to −5.26 mmolC m−2 d−1) and a source during high river flow (5.71 to 19.37 mmolC m−2 d−1). In the mangrove creek, the pCO2, DIC, δ13C-DIC and TA presented deviations from the conservativity, with slopes between TA and DIC demonstrating organic carbon degradation mediated by aerobic respiration and sulphate reduction. Mangrove creek waters were a CO2 source (average of 134.81 mmolC m−2 d−1), exhibiting high values of pCO2 (up to 21,720 ppmv). The results reveal that the low buffering capacity in the main channel of tropical estuarine deltas can be the predominant driver of pCO2, generating CO2 undersaturation along the mixing zone, a process overlooked in estuarine systems. Moreover, air-water CO2 exchange, thermal variability, and biological activities contribute to deviation of the carbonate system from conservative mixing in specific estuarine areas, also modulating pCO2 variability.