As part of the endless efforts exerted by Channel Maintenance Research Institute, (CMRI) researchers have reached an innovative technique to convert different types of wastes such as water weeds into bio-gas and organic fertilizers in an attempt to reduce water and agricultural land pollution. Since all types of wastes like agriculture residues, animal manure and water weeds are considered non recycled materials. There have emerged several problems of water weeds; such as: blocking the watercourses and altering water quality and quantity, increasing water losses, burning weeds causes medical problems, providing suitable environment for insects and diseases, and finally difficulties in navigation, fisheries, and maintaining irrigation pumps. In this regard, Egypt has a pioneer experience in converting water weeds into biogas and organic fertilizers using different types of biogas units basically in Behara and Kafr ElSheikh Governorates. Also, several workshops and practical trainings were organized on applying organic fertilizers instead of chemical fertilizers. On the other hand, the Egyptian experience has been implemented in Uganda at Lakes Kyoga and Albert where there are many challenges; i.e. increasing deposition, difficulties in getting water for drinking and domestic usages, difficulties in fishing activities, and the environment is suitable for diseases such as Malaria. It's worth mentioning that the role of Egypt in the Egyptian-Ugandan project is mainly focused on the maintenance of Kyoga and Albert lakes to controlling the growth of water weeds. Channel Maintenance Research Institute was responsible for converting the removed weeds into biogas and organic fertilizers. The biogas is thus used in domestic uses such as cooking, where gas meters have been installed in each house to measure natural gas consumption/houses. Capacity building for Ugandan engineers and stakeholders has also taken place by means of training courses, workshops and meetings.