AbstractWetlands impact global warming by regulating the atmospheric exchange of greenhouse gases (GHGs), including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). We investigated GHG emissions in the Great Lakes coastal wetlands across various hydrologic, temperature, and nitrogen (N) inflow regimes using a process‐based simulation model. We found the emission of CH4, N2O, and sequestration of C (i.e., negative net ecosystem exchange, NEE) in our simulations were all positively related to water residence time and N inflow, primarily due to greater plant productivity and N uptake, which facilitated greater C and N cycling rates in the model. Water level scenarios also had an effect on GHG exchanges by moderating the transitions between aerobic and anaerobic conditions. Temperature effects on GHGs were minimal compared with other factors. The net sustained‐flux global warming potential (SGWP; i.e., sum SGWP of CH4, N2O, and NEE) of wetlands on 20‐year and 100‐year time horizons were both primarily driven by CH4 emissions and strongly controlled by the tradeoffs between CH4 emission and CO2 sequestration, with a negligible amount of simulated N2O emissions. Future research could include model enhancements to provide increased process‐level details on the aerobic‐anaerobic transitions or the direct effects of plants on mediating GHG exchanges. Field studies addressing the interaction of N inflows and water residence time at appropriately large scales are needed to test the complex interactions revealed by our modeling study. Our results highlight the previously under‐appreciated role of nitrogen and water residence time in modulating SGWP in coastal wetlands.