The Nile basin countries, particularly those in the downstream are experiencing water poverty due to the rapid growth in population and climate change. This water scarcity conditions highlighted the vast amount of water losses occurring in the swampy areas of the Nile River basin. Saving these water losses becomes a real hope to reduce the food gap and promote development in all Nile Basin countries. Jonglei Canal is one of the most important projects which were proposed to save the water losses in the Sudd region in Southern Sudan. The project was launched and stopped in 1980S due to civil war in Sudan. Recently the upper riparian Nile countries have declared their plans for potential development projects which might significantly reduce the flow to the Sudd region and hence the potential water savings from Jonglei Canal. Environmental concerns have also been declared by the local tribes living in the area that the size of the swampy areas will be reduced which will adversely affect their grazing activities. This paper investigates the impact of the development projects in the Upstream countries on the feasibility of the Jonglei Canal Project. The size of the swampy area is quantified under different scenarios of upstream development and Jonglei canal operation. Nile Decision Support Tool (Nile DST model) and HEC-RAS model have been utilized for hydrologic and hydraulic simulations of the White Nile System. It is found that any further expansion in the irrigation projects in the Upstream countries in the future may affect the water benefits of Jonglei canal project. The hydraulic simulations indicated that the existing cross-sections of Jonglei canal are adequate and need not to be modified. The reduction in the swampy area due to Jonglei canal was found on the order of only 7%, which may increase to 16% under the upstream development.