Wetland ecosystems are an important component in global carbon (C) cycles and may exert a large influence on global climate change. Predictions of C dynamics require us to consider interactions among many critical factors of soil, hydrology, and vegetation. However, few such integrated C models exist for wetland ecosystems. In this paper, we report a simulation model, Wetland-DNDC, for C dynamics and methane (CH4) emissions in wetland ecosystems. The general structure of Wetland-DNDC was adopted from PnET-N-DNDC, a process-oriented biogeochemical model that simulates C and N dynamics in upland forest ecosystems. Several new functions and algorithms were developed for Wetland-DNDC to capture the unique features of wetland ecosystems, such as water table dynamics, growth of mosses and herbaceous plants, and soil biogeochemical processes under anaerobic conditions. The model has been validated against various observations from three wetland sites in Northern America. The validation results are in agreement with the measurements of water table dynamics, soil temperature, CH4 fluxes, net ecosystem productivity (NEP), and annual C budgets. Sensitivity analysis indicates that the most critical input factors for C dynamics in the wetland ecosystems are air temperature, water outflow parameters, initial soil C content, and plant photosynthesis capacity. NEP and CH4 emissions are sensitive to many of the tested input variables. By integrating the primary drivers of climate, hydrology, soil and vegetation, the Wetland-DNDC model is capable of predicting C biogeochemical cycles in wetland ecosystems.