Lakes George and Edward are small water bodies located in the western arm of the East African Rift Valley. Lake George is a small (250 km2) shallow water (mean depth 2.5 metre) system and is wholly located in Uganda. Lake Edward is much larger (2325 km2), deeper water body with an average depth of 34 metres and maximum depth of 112 metres (UNDF, 2013) and is shared between Uganda (29%) and DR Congo (71%) (Beadle, 1966). Both lakes are drained by several rivers and streams from the Rwenzori Mountains and from the rich agricultural areas to the north east. The two lakes are linked with each other by a 40km long Kazinga Channel. The lakes harbor a number of fish species of which three, the Nile tilapia, Oreochromis niloticus, the African catfish, Clarias gariepinus and the Semutundu, Bagrus docmac were the subject of this study. The objective of the study was to investigate the natural feeding interactions between key commercial fish species and the available natural food sources, namely the algae, zooplankton, macro-benthos and prey fishes and establish the potential of the two lake environments and the food resources therein to sustain high fish productivity.