The lakes and waterways of East Africa that provide the greatest expanse of inland water in the tropics represent untapped potential for transport and logistics. Countries in East Africa have recognized this potential and have been reviving the Inland Waterway Transport (IWT) sector to meet the rising demand for transport and logistics and support the implementation of the African Continental Free Trade Area (AfCFTA). Through best practices from international experience and transport development trends, East Africa has embraced an integrated multi-modal corridor approach and leapfrogged IWT development. The subregion has two main multi-modal corridors – the Northern Corridor and the Central Corridor. Based on the insights drawn from the comparative analysis of best practices and lessons learned from African and international case studies, recommendations for enhancing the operational capabilities for logistics and transportation for inland waterways and lakes in Eastern Africa are provided in categories. Although Eastern Africa, according to classification by the United Nations Economic Commission for Africa (ECA), covers 14 countries, the focus of this paper are those countries listed with major lakes and waterways. They include Burundi, DRC, Kenya, Rwanda, South Sudan, Tanzania and Uganda. The lakes and waterways of Eastern Africa represent untapped potential for logistics and transportation. They are also home to some of the largest and most ecologically diverse freshwater systems in the world, supporting millions of people with drinking water, food and livelihoods. Thus, the protection, conservation and sustainable management of blue assets, and development for logistics and transportation must go hand in hand.