Wetland water depth influences microbial and plant communities, which can alter the above- and below-ground carbon cycling of a wetland. Wetland water depths are likely to change due to shifting precipitation patterns, which will affect projections of greenhouse gas emissions; however, these effects are rarely incorporated into wetland greenhouse gas models. Seeking to address this gap, we used a mechanistic model, ecosys, to simulate a range of water depth scenarios in a temperate wetland, and analyzed simulated predictions of carbon dioxide (CO₂) and methane (CH₄) fluxes over the 21st century. We tested our model using eddy covariance measurements of CO₂ and CH₄ fluxes collected at the Old Woman Creek National Estuarine Research Reserve (OWC) during 2015 and 2016. OWC is a lacustrine, estuarine, freshwater, mineral-soil marsh. An empirical model found that the wetland water depth is highly dependent on the water depth of the nearby Lake Erie. Future wetland surface water depths were modeled based on projection of Lake Erie's water depth using four separate NOAA projections, resulting in four wetland water-depth scenarios. Two of the four 21st century projections for Lake Erie water depths used in this study indicated that the water depth of the wetland would remain nearly steady; however, the other two indicated decreases in the wetland water depth. In our scenario where the wetland dries out, we project the wetland's climatological warming effect will decrease due to smaller CH₄ fluxes to the atmosphere and larger CO₂ uptake by the wetland. We also found that increased water level can lower emissions by shifting the site towards more open water areas, which have lower CH₄ emissions. We found that decreased water depths would cause more widespread colonization of the wetland by macrophyte vegetation. Using an empirical relationship, we also found that further drying could result in other, non-wetland vegetation to emerge, dramatically altering soil carbon cycling. In three of our four projections, we found that in general the magnitude of CO₂ and CH₄ fluxes steadily increase over the next 100 years in response to higher temperatures. However, in our driest simulations, we projected a different response due to increased oxidation of soil carbon, with CH₄ emissions decreasing substantially from an annual cumulative peak of 224.6 to a minimum of 104.7 gC m^-2 year^-1. In that same simulation, net cumulative flux of CO₂ changed from being a sink of 56.5 gC m^-2 year^-1 to a source of 369.6 gC m^-2 year^-1 over the same period, despite a temperature increase from 13.7 °C to 14.2 °C. This temperature shift in our other three cases with greater water depths increased the source strength of CH₄ and the sink strength of CO₂. We conclude that the magnitude of wetland greenhouse-gas fluxes depended on the water depth primarily as it affected the areal percentage of the wetland available for plant colonization, but dramatic decreases in water depths could cause significant reductions in the wetland CH₄ fluxes, while simultaneously altering the wetland vegetation.