The lake is nowhere deeper than about 5.7 meters, and most of it is less than 4 m in depth. Areas less than 3 m deep are completely covered by water lilies, while much of swampy shoreline is covered with papyrus. The papyrus also forms floating islands that drift between a number of small permanent islands.
46 species of fish have been recorded in Lake Kyoga, and crocodiles are numerous.