We report a data set of biogeochemical variables related to carbon cycling obtained in the three branches (My˜ Tho, Hàm Luông, Co^´ Chiên) of the Mekong delta (Be^´n Tre province, Vietnam) in December 2003, April 2004, and October 2004. Both the inner estuary (upstream of the mouth) and the outer estuary (river plume) were sampled, as well as side channels. The values of the partial pressure of CO2 (pCO2) ranged between 232 and 4085 ppm, O2 saturation level (%O2) between 63 and 114 %, and CH4 between 2 and 2217 nmol L−1, within the ranges of values previously reported in temperate and tropical meso- and macro-tidal estuaries. Strong seasonal variations were observed. In the upper oligohaline estuary, low pCO2 (479–753 ppm) and high %O2 (98–106 %) values were observed in April 2004 most probably related to freshwater phytoplankton growth owing to low freshwater discharge (1400 m3 s−1) and increase in water residence time; during the two other sampling periods with a higher freshwater discharge (9300–17 900 m3 s−1), higher pCO2 (1895–2664 ppm) and lower %O2 (69–84 %) values were observed in the oligohaline part of the estuary. In October 2004, important phytoplankton growth occurred in the offshore part of the river plume as attested by changes in the contribution of particulate organic carbon (POC) to total suspended matter (TSM) (%POC) and the stable isotope composition of POC (δ13C-POC), possibly related to low TSM values (improvement of light conditions for phytoplankton development), leading to low pCO2 (232 ppm) and high %O2 (114 %) values. Water in the side channels in the Mekong delta was strongly impacted by inputs from the extensive shrimp farming ponds. The values of pCO2, CH4, %O2, and the stable isotope composition of dissolved inorganic carbon (δ13C-DIC) indicated intense organic matter degradation that was partly mediated by sulfate reduction in sediments, as revealed by the slope of total alkalinity (TA) and DIC covariations. The δ13C-POC variations also indicated intense phytoplankton growth in the side channels, presumably due to nutrient enrichment related to the shrimp farming ponds. A data set in the mangrove creeks of the Ca Mau province (part of the Mekong delta) was also acquired in April and October 2004. These data extended the range of variability in pCO2 and %O2 with more extreme values than in the Mekong delta (Be^´n Tre), with maxima and minima of 6912 ppm and 37 %, respectively. Similarly, the maximum CH4 concentration (686 nmol L−1) was higher in the Ca Mau province mangrove creeks than in the Mekong delta (Be^´n Tre, maximum 222 nmol L−1) during the October 2004 cruise (rainy season and high freshwater discharge period). In April 2004 (dry season and low freshwater discharge period), the CH4 values were much lower than in October 2004 (average 19 ± 13 and 210 ± 158 nmol L−1, respectively) in the Ca Mau province mangrove creeks, owing to the higher salinity (average 33.2 ± 0.6 and 14.1 ± 1.2, respectively) that probably led to higher sediment sulfate reduction, leading to inhibition of sediment methanogenesis and higher anaerobic CH4 oxidation. In the inner estuarine region (three branches of the Mekong delta), CO2 emissions to the atmosphere averaged 121 mmol m−2 d−1, and the CH4 emissions averaged 118 µmol m−2 d−1. The CO2 emission to the atmosphere from the Mekong inner estuary was higher than reported in the Yangtze and Pearl river inner estuaries. This was probably due to the lower salinity in the Mekong delta branches, possibly due to different morphology: relatively linear channels in the Mekong delta versus funnel-shaped estuaries for the Yangtze and Pearl river inner estuaries.< Leer menos