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In this article, extension and application to variably saturated wetland conditions of a process-based wetland model is demonstrated. The new model described in this article is an improved version of an earlier model, which was only capable of capturing nutrient dynamics in continuously ponded wetlands. The upgraded model is capable of simulating nutrient cycling and biogeochemical reactions in both ponded and unsaturated wetland zones. To accomplish this goal, a comprehensive module for tracking water content in wetland soil was implemented in the model, and biogeochemical relationships were added to explain cycling of nitrogen (N) and carbon (C) in variably saturated zones of wetlands. The developed model was applied to a small, restored wetland receiving agricultural runoff, located on Kent Island, Maryland. On average, during the two-year study period, the ponded compartment of the study wetland covered 65% of the total 1.2 ha area. Through mass balance analysis, it was revealed that the mass of nitrogen lost to denitrification at the variably saturated compartment of the study wetland was about three times higher than that of the ponded compartment (32.7 +/- 29.3 kg versus 9.5 +/- 5.5 kg), whereas ammonia volatilization at the variably saturated compartment was a fraction of that of ponded compartment (1.2 +/- 1.9 kg versus 11.3 +/- 11.8 kg). Sensitivity analysis showed that cycling of carbon-related constituents in variably saturated compartment had high sensitivity to temperature and available soil moisture. (C) 2016 American Society of Civil Engineers.