The variable hydrology of freshwater wetlands fuels a dynamic biogeochemical regime, in which the degree of inundation influences oxygen availability within the water column and sediments. These hydrologically mediated oxygen conditions govern aerobic and anaerobic microbial pathways that directly influence the production and emission of carbon dioxide (CO₂) and methane (CH₄). Although hydrology, vegetation, and organic matter availability are well-established drivers of wetland greenhouse gas emissions, the seasonal variability of these controls and their effects on CO₂ and CH₄ fluxes remain understudied. We hypothesized that wetlands with longer periods of inundation are often dominated by anoxia which can cause increases in methane (CH4) production, while drier wetlands are often characterized by increased carbon dioxide (CO2) emissions due to increased aerobic respiration from higher oxygen availability. This study quantified CO₂ and CH₄ emissions from a geographically isolated wetland during peak inundation through complete drying (March–June) as water levels transitioned from inundated to exposed sediments. Our study wetland was an 18-acre cypress swamp located within a managed longleaf pine forest at The Jones Center at Ichauway in southwest Georgia. We collected in-situ emission data from water and sediment surfaces using floating and soil chambers placed throughout our study wetland along transects from the dry wetland perimeter to the deepest point of inundation in the wetland. Total CO2 and CH4 emission rates were calculated based on chamber gas accumulation rates and averaged for each site along the transect. Results showed higher mean CH4 emissions at the deepest water levels consistently throughout the three months of this study. CO2 emissions were highest at our perimeter sites where we measured soil gas accumulation. Our results highlight the seasonal variability of GHG emissions in southeastern wetlands and demonstrate the influence of hydrologic variation on these emissions.