River Nile is one of the longest transboundery rivers and it is shared and used by Burundi, Democratic Republic of Congo, Egypt, Ethiopia, Eritrea, Kenya, Rwanda, Sudan, Tanzania and Uganda. As of today, the Nile is a crucial resource for the economic development of the Nile Basin countries and a vital source of livelihood for 160 million inhabitants as well as 300 million people living in the 10 riparian countries. The Nile Basin Initiative (NBI) is one of the international cooperative river basin management program and regional partnership where all the Nile Basin countries except Eritrea unite to pursue long-term sustainable development, improved land use practices and management. This review therefore focused on the challenges not faced on NBI in terms of integrated use of the river and conducted analysis of strengths, weaknesses, opportunities and threats (SWOT) based on secondary data. The result of the review revealed that for decades, the Nile Basin people have been facing many complex environmental, social, economic and political challenges that have made it difficult for the proper management and sustainability of Nile water. The initiative provides training to develop skills in government ministries, non-governmental organizations and local communities in each country. It is also working to raise awareness of critical environmental issues by strengthening networks of environmental education practitioners; developing curriculum in the education sector. The challenges of NBI include the involvement and funding of World Bank, lack of sufficient staff, procedural and policies conflicts, lack of coordination and linkage with other regional institutions and lack of recognition as river basin organization. Considering the complex nature of the project, it is recommended that the NBI should come up with a strong multi-disciplinary monitoring and evaluation team to follow up all implemented projects. The NBI should carry out participatory land use planning in communities along the river basin. Moreover, livelihood analysis should be carried out especially in communities along the Nile to come up with poverty eradication projects which are socially acceptable, applicable, economically viable and affordable.