Though wetlands are recognized for their wide range of ecosystem services, the sustainable management of wetlands is hindered by a lack of data, especially in large transnational river systems in less-developed countries. The Sudd wetland of South Sudan is the largest freshwater wetland on the Nile River and supports transhumant pastoral cultures and wildlife migrations; yet, it is understudied in terms of its regional hydrologic controls and corresponding changes in land cover. To assess the use of remote data derived from remote sensing systems, the wetland extent between 2000 and 2014 was delineated using MODIS thermal infrared data and baseline changes in the wetland land cover extents were mapped using NDVI products. The upper White Nile basin was subdivided into seven natural sub-basins and correlations between sub-basin precipitation amounts and wetland extents were determined. Areas of high spatial variability in land cover were related to the spatial distribution of conflict in South Sudan. Results indicate that downstream sub-basins, which have largely been ignored, display high correlations (0.58–0.74) with the wetland extent and appear to be major sources of water for the wetland. Precipitation patterns in the Lake Kyoga sub-basin, instead of the neighboring torrent sub-basin that has previously been cited, correspond to inter-annual changes in wetland extents. Land cover transitions in years of reduced flow amounts varied depending upon the precipitation in upstream and downstream sub-basins. Because the downstream sub-basins appear to have a higher influence than previously anticipated, a reduction in water from the upstream sub-basins didn't necessarily lead to a reduced wetland extent. The most highly variable regions of land cover changes correspond not only to locations of conflict, but also to ethnic boundary lines. Though the conflict in this region makes in-situ data collection difficult, the conflict only increases the need for scientific assessments in order to predict changes in ecosystem services.