Projecting permafrost carbon climate feedback largely depends on model representation of permafrost, permafrost thaw-associated local hydrological change, and the link between biogeophysics and biogeochemistry. Our previous work showed the effects of incorporating ‘excess ice’ in the Community Land Model (CLM) and how excess ice and subsequent melting of excess ice under warming climate affects energy and hydrological cycles within the model. Here, we develop permafrost affected wetlands with melting of excess ice by using gridcell microtopography to better link permafrost thaw and subsequent methane (CH4) dynamics. Our model development will allow more realistic simulations of permafrost thaw related processes within the Earth System Model by global scale simulations such as permafrost thaw, thermokarst formation, Arctic wetland formation and seasonal cycles, and CH4 dynamics. Finally, a newly funded project allows continuous observations of CO2 and CH4 in soil profiles, which will be used in evaluations of model simulations.