The objective of this research is to investigate incorporating a wetland component into a land energy and water fluxes model, the Community Land Model (CLM). CLM is the land fluxes component of the Integrated Global Systems Model (IGSM), a framework that simulates the relationship of physical systems to climate variations. Wetlands play an important role in the storage and regulation of the global water budget so including them in a land water cycle model is found to be necessary in balancing the regional water budgets of simulated river basins. This research focuses on modeling broad hydrological characteristics of wetlands (and lakes) into CLM. CLM’s wetland component is reconstructed to reflect a more realistic wetland water budget; it allows for the exchange of water with CLM’s river routing component; it allows for varying the storage of wetlands; it allows for calculating discharge from wetlands based on the physics of these ecosystems; and allows the surface water extent of wetlands to vary, a characteristic important to ecological behavior of wetlands and management of wetland ecosystems. The research then implements the modified version of the model for the Sudd wetland, in South Sudan, as it relates to its larger river system, the White Nile. Projects designed to better manage this wetland, such as diverting its inflow to reduce the amount of water consumed by evaporation, are currently under review by its various stakeholders. This diversion stands to change the area of the Sudd, which has direct implications on the ecological and social services derived from the wetland locally. The modified CLM is thus used to provide a better understanding of the science of this management option, and furthers the discussion on the benefits or drawbacks to diversion. Thus, using area as a proxy for environmental impact, what are the environmental, economic and social risks associated with diverting water from inflow into the Sudd? The new wetland component’s performance is evaluated against existing observed and modeled data on Sudd hydrology and compared to existing models of the Sudd. The research finds that the potential benefits of diversion cannot be said to unequivocally better the larger system of the White Nile.