|Wetlands possess qualities that distinguish them as the most important influencer of global carbon (C) budgets. They have the highest carbon density among all terrestrial ecosystems and are known as the greatest individual source of methane emission to the atmosphere. Because of this great influence, considerable scientific efforts have been invested in wetland models, with the objective of quantifying wetland C storage, turnover and carbon interchanges between wetland soils and atmosphere. This study, performed in three stages, was undertaken to advance the current state of wetland modeling by introducing a comprehensive mechanistic wetland carbon cycling model. In stage one, I developed and validated a process based model for carbon cycling in flooded wetlands, called WetQual-C. WetQual-C reflects various biogeochemical interactions affecting C cycling in flooded wetlands, and is capable of simulating the dynamics of organic carbon (OC) retention, OC export and greenhouse gas (GHG) emissions on the same platform. Using field collected data from a small wetland on the eastern shore of Chesapeake Bay, model performance was assessed and a thorough sensitivity and uncertainty analysis was carried out. Overall, the model performed well in capturing total organic carbon (TOC) export dynamics from the study wetland. Model results revealed that over a period of 2 years, the wetland removed or retained 47 ± 12% of the OC carbon intake, mostly via OC decomposition and dissolved organic carbon (DOC) diffusion to sediment. In the second stage of this study, I expanded WetQual model’s spatial resolution through compartmentalization of the model, in order to capture the spatial variability of constituent concentrations in water and sediment of various zones in the wetland. The compartmental model was applied to data collected from a restored wetland in California’s Central Valley during the 2007 growing season. The study wetland had a formation of a large stagnant zone at the southern end which constituted more than 50% of the wetland area. Mass balance analysis revealed that over the course of the study period, about 23.4 ± 3.9% of the incoming total nitrogen (TN) load and 21.1 ± 4.4% of the TOC load was removed or retained by the study wetland. It was observed that mass of all exchanges (physical and biogeochemical) regarding nitrogen and carbon cycling decreased along the activity gradient from active to passive zones of the wetland. In the third stage of this study, I further extended WetQual capabilities to simulate geochemical reactions in parts of the wetland that are not flooded (unsaturated wetland soil). To accomplish such goal, a comprehensive module for tracking soil moisture in wetland soil was implemented, and model relationships were updated to simulate geochemical reactions of nitrogen, carbon and phosphorus related constituents in unsaturated wetland soil. The developed model was applied to a small restored wetland located on Kent Island, Maryland. On average, the ponded compartment of the study wetland covered 65% of the total 1.2 ha area. Through mass balance analysis, it was revealed that denitrification in the unsaturated compartment of the study wetland was approximately 3 times higher than that of the ponded compartment (32.7 ± 29.3 kg vs. 9.5 ± 5.5 kg) whereas ammonia volatilization in the unsaturated compartment was a fraction of that of ponded compartment.