We improved the realism of wetland representation in the U.S. Department of Energy’s Exascale Earth System Model (E3SM) Land-surface Model (ELM). We develop an updated version, ELM-Wet, where we activate a separate wet-landunit for wetlands that handles multiple eco-hydrological functional type patches. We introduced a wetland-specific hydrology through prescribing site-level (whole wetland) constraints on surface water elevation and including a patch-level characteristic maximal inundation depth that enables resolving different sustained inundation depth for different patches, and if data exists, prescribing inundation depth at the site and patch levels. We modified the calculation of aerenchyma transport diffusivity based on observed conductance for different vegetation types. We use BOA, a new Bayesian Optimization toolpack, to parameterize CO₂ and CH₄ fluxes in the wetland landunit. Site-level simulations of a coastal freshwater wetland in Louisiana (US-LA2) were performed with the updated model. Eddy covariance observations of CO₂ and CH₄ fluxes from 2012-2013 were used to train the model. Flux data from 2021 were used for validation. Patch-specific chamber flux observations and observations of CH₄ concentration profiles in the soil porewater from 2021 were used for evaluation of the model performance in terms of fluxes and soil concentration profiles at the patch level. Our results show that ELM-Wet with BOA optimization and prescribed inundation reduced the model’s predicted CH₄ emission error by up to 33%. The updated model was able to represent inter-daily and seasonal CO₂ and CH₄ flux and concentration dynamics across the wetland’s eco-hydrological patches.