The African Great Lakes region has been experiencing extreme rainfall. Sometimes, it might result in floods or it might be very dry weather. But by 2050 the whole region will be experiencing significant changes in the water cycle. Water is the lifeblood of this region with large lakes and rivers. The state of water resources affects all natural, social and economic systems. Water serves as the fundamental link between the climate system, human society and the environment. Climate change is severely impacting the hydrological cycle and consequently, water management in the region. This will in turn have significant effects on human development and security of the people of the Great Lakes region. Last year, the United Nations reached an historic agreement on the 2030 Agenda for Sustainable Development, which includes a dedicated Sustainable Development Goal on water and sanitation that calls for ensuring the availability and sustainable management of water and sanitation for all. The world now has also a universal, fair, flexible and durable climate agreement. The countries of the Great Lakes Region are now moving towards development models that are more sustainable, protecting the environment and addressing climate change in the region. But climate change threatens to undermine or even roll back gains we have made in the management of Great Lakes and their basins. And its impacts are expected to be felt more clearly on our water resources resulting in increased or more frequent flooding and drought which threaten the very foundation of our ability to ensure food, energy, health and jobs for all the people of the African Great Lakes region. This paper addresses emerging and persisting challenges to improve water quality, pollution and better waste management. In addition, the proposed water SDG that includes targets on increased water-use efficiency, integrated water resources management and the protection of water-related ecosystems in the African Great Lakes region.