Emissions of methane (CH₄) and nitrous oxide (N₂O) from soils to the atmosphere can offset the benefits of carbon sequestration for climate change mitigation. While past study has suggested that both CH₄ and N₂O emissions from tidal freshwater forested wetlands (TFFW) are generally low, the impacts of coastal droughts and drought-induced saltwater intrusion on CH₄ and N₂O emissions remain unclear. In this study, a process-driven biogeochemistry model, Tidal Freshwater Wetland DeNitrification-DeComposition (TFW-DNDC) was applied to examine the responses of CH₄ and N₂O emissions to episodic drought-induced saltwater intrusion in TFFW along the Waccamaw River and Savannah River, USA. These sites encompass landscape gradients of both surface and porewater salinity as influenced by Atlantic Ocean tides superimposed on periodic droughts. Surprisingly, CH₄ and N₂O emission responsiveness to coastal droughts and drought-induced saltwater intrusion varied greatly between river systems and among local geomorphologic settings. This reflected the complexity of wetland CH₄ and N₂O emissions and suggests that simple linkages to salinity may not always be relevant, as non-linear relationships dominated our simulations. Along the Savannah River, N₂O emissions in the moderate-oligohaline tidal forest site tended to increase dramatically under the drought condition, while CH₄ emission decreased. For the Waccamaw River, emissions of both CH₄ and N₂O in the moderate-oligohaline tidal forest site tended to decrease under the drought condition, but the capacity of the moderate-oligohaline tidal forest to serve as a carbon sink was substantially reduced due to significant declines in net primary productivity and soil organic carbon sequestration rates as salinity killed the dominant freshwater vegetation. These changes in fluxes of CH₄ and N₂O reflect crucial synergistic effects of soil salinity and water level on C and N dynamics in TFFW due to drought-induced seawater intrusion.