© 2015 American Society of Civil Engineers. A common phenomenon observed in natural and constructed wetlands is short-circuiting of flow and formation of stagnant zones that are only indirectly connected with the incoming water. Biogeochemistry of passive areas is potentially much different than that of active zones. In the research reported in this paper, the spatial resolution of a previously developed wetland nutrient cycling model was improved in order to capture the spatial variability of concentrations and reaction rates regarding nitrogen and carbon cycles throughout active and passive zones of wetlands. The upgraded model allows for several compartments in the horizontal domain, with all neighboring compartments connected through advective and dispersive/diffusive mass transport. The model was applied to data collected from a restored wetland in California that was characterized by the formation of a large stagnant zone at the southern end of the wetland due to close vicinity of the inlet and outlet structures in the northern end. Mass balance analysis revealed that over the course of the research period, about 23.4±3.9% of the incoming total nitrogen load was removed or retained by the wetland. It was observed that mass of all exchanges (physical and biogeochemical) regarding nitrogen cycling decreased along the activity gradient from active to passive zones. Model results also revealed that anaerobic processes become more significant along the activity gradient towards passive areas.