We performed a preliminary study to quantify CO2 and CH4 emissions from the water column within a Rhizophora spp. mangrove forest. Mean CO2 and CH4 emissions during the studied period were 3.35 ± 3.62 mmolC m−2 h−1 and 18.30 ± 27.72 μmolC m−2 h−1, respectively. CO2 and CH4 emissions were highly variable and mainly driven by tides (flow/ebb, water column thickness, neap/spring). Indeed, an inverse relationship between the magnitude of the emissions and the thickness of the water column above the mangrove soil was observed. δ13CO2 values ranged from −26.88‰ to −8.6‰, suggesting a mixing between CO2-enriched pore waters and lagoon incoming waters. In addition, CO2 and CH4 emissions were significantly higher during ebb tides, mainly due to the progressive enrichment of the water column by diffusive fluxes as its residence time over the forest floor increased. Eventually, we observed higher CO2 and CH4 emissions during spring tides than during neap tides, combined to depleted δ13CO2 values, suggesting a higher contribution of soil-produced gases to the emissions. These higher emissions may result from higher renewable of the electron acceptor and enhanced exchange surface between the soil and the water column. This study shows that CO2 and CH4 emissions from the water column were not negligible and must be considered in future carbon budgets in mangroves.