There is a growing interest in how the management of ‘blue carbon’ sequestered by coastal wetlands can influence global greenhouse gas (GHG) budgets. A promising intervention is through restoring tidal exchange to impounded coastal wetlands for reduced methane (CH4 ) emissions. We monitored an impounded wetland’s GHG flux (CO2 and CH4 ) prior to and following tidal reinstatement. We found that biogeochemical responses varied across an elevation gradient. The low elevation zone experienced a greater increase in water level and an associated greater marine transition in the sediment microbial community (16 S rRNA) than the high elevation zone. The low elevation zone’s GHG emissions had a reduced sustained global warming potential of 264 g m−2 yr−1 CO2-e over 100 years, and it increased to 351 g m−2 yr−1 with the removal of extreme rain events. However, emission benefits were achieved through a reduction in CO2 emissions, not CH4 emissions. Overall, the wetland shifted from a prior CH4 sink (−0.07 to −1.74 g C m−2 yr−1 ) to a variable sink or source depending on the elevation site and rainfall. This highlights the need to consider a wetland’s initial GHG emissions, elevation and future rainfall trends when assessing the efficacy of tidal reinstatement for GHG emission control.