Despite the importance of peatlands in the global carbon cycle, no widely applicable ecosystem model exists for peatlands. Simulations of three montane fens in Colorado, USA were conducted to test the capabilities of the CENTURY ecosystem model to simulate 1) long-term carbon accumulation and 2) short-term changes in carbon accumulation due to hydrologic changes. The CENTURY model was calibrated to simulate long-term carbon accumulation in two fens for up to 10,000 years by adjusting three variables that represent anaerobic soil conditions. CENTURY was unable to simulate long-term carbon accumulation in a third fen using settings for the two calibrated fens. However, CENTURY correctly simulated total carbon storage by adjusting two of the three anaerobic variables. A sensitivity analysis revealed that carbon accumulation in CENTURY is highly sensitive to anaerobic soil conditions. CENTURY predicted that half of the fen peat is composed of structural root material. The majority of the remaining peat was composed of recalcitrant slow and passive soil organic matter. Precipitation levels were altered to determine if CENTURY could predict the change in carbon accumulation rates due to periodic drier conditions. The simulated drying scenario predicted an average carbon loss of 70 g C m⁻² yr⁻¹ during the 100-year simulation. The loss of carbon occurred despite plant production increasing from an average of 249 g C m⁻² yr⁻¹ to 391 g C m⁻² yr⁻¹. Slightly more than 90% of the carbon lost was from the structural root pool and slow organic matter pool, while there was no carbon loss or a slight net carbon gain in the passive organic matter pool and above-ground structural and metabolic pools. Despite several shortcomings, our results indicate that an ecosystem model, such as CENTURY, can be useful for simulating carbon dynamics in peatlands.