Management of complex and international water bodies, e.g. Nile River and Lake Victoria, has to take in consideration the multiple benefits and the diverse interests of stakeholders of the countries sharing such common resources. Most often such rersources are understood as water resources while there are many other strategic values of benefits for other sectors, e.g. energy, tourism, transport, agriculture, industry, ..... . The national use and abuse of such international, common and complex natural resources has dynamic short-term and long-term impacts on status of water and associated ecology on the whole water body. Understanding of the functioning and metabolism of such complex water systems has to based on comprehensive studies of the spatio-temporal changes in these systems from natural changes (environmental and climate) and human activities (waste, sanitation, industrial, tourism, transport, ....... etc.