Subtropical and tropical wetlands play a prominent role in the global carbon (C) cycle; yet factors that influence their C fluxes remain uncertain. We collected measurements from a temporarily flooded subtropical wetland over 3 years to investigate environmental drivers impacting CO2 and CH4 fluxes. The wetland was a sink of CO2 (−469 to −380 g C‐CO2 · m−2 · year−1) and a source of CH4 (25.1 to 32.1 g C‐CH4 · m−2 · year−1) to the atmosphere. Dry season CH4 emissions represented 41 to 49% of the annual budget, reflecting the importance of continuous CH4 flux measurements. Gross primary productivity (GPP) increased with temperature and radiation, and the influence of VPD on GPP varied with soil inundation. Higher water tables decreased Reco and increased GPP, and a higher GPP in turn lead to enhanced Reco likely through enhancements of GPP on autotrophic respiration. This suggests that the impact of the water table on Reco depends on the cancelling effects of hydrology and GPP. Emissions of CH4 increased with soil temperature, water table, and GPP until soils were inundated at which point temperature and GPP became the main drivers. Water table and temperature influenced GPP and CH4 fluxes, and increases in GPP directly enhanced CH4 emissions. In addition to impacting C fluxes directly through water table depth, hydrology also determined the hierarchy of the dominance of factors controlling C fluxes and their response. The positive climate forcing of subtropical wetlands may be dictated by plant‐mediated and climate interactions, with hydrological factors playing a major role in determining the greenhouse gas sink or source strength of subtropical wetlands.