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Mangrove water biogeochemistry has been frequently studied under tropical climates, but less is known regarding mangroves in semi-arid climates. In this study, we examine the carbon and nutrient biogeochemistry in a mangrove tidal creek and in the main branch of a semi-arid estuary in New Caledonia. Porewater seepage represents a source of nutrients (DON, NH4 (+), and DIP), carbon (DOC and CO2), and alkalinity for the water column, but seawater dilution of the mangrove inputs is observed. Spatial and tidal variations in CO2 fluxes along the tidal creek suggest that porewater seepage is a driver of CO2 emission into the atmosphere. Large seasonal and spatial differences in the biogeochemical functioning of the main channel are observed and are mainly related to the seasonal rainfall pattern. During the rainy season, the watershed influences the entire estuary, which exhibits a typical positive circulation. During the dry season, the estuary turns into a salt-plug region with positive and negative circulations in the upper and lower reaches, respectively. In this case, the upper and lower reaches seem to function independently, and the biogeochemical functioning of their water column is not controlled by the same processes. Surprisingly, pCO(2)@27 A degrees C values tend to be higher during the dry season, as do the total alkalinity (TAlk) values, while the pH values exhibit an opposite trend. Moreover, the TAlk values are higher in the lower reaches during the wet season and in the upper reaches during the dry season. These results indicate high in situ biogeochemical reactions and high porewater influence during the dry season, likely because of a low flushing rate and high water residence time after salt plug establishment. Although our results suggest that salt plugs may significantly affect the water column’s biogeochemistry and may promote CO2 emissions of mangrove-derived carbon, further investigations, especially mass balance studies, are required to quantify their role in the biogeochemical functioning of such estuarine systems.