Lake Kyoga is as a result of faulting which led to both upward and downward warping which eventually resulted into the formation of the East African rift valley where this lake is found. River Kafu once flowing westwards began to flow eastwards. Lake Kyoga was then formed by ponding-back of the Kafu river. The lake lies in the flooded branches of the low west-flowing Kafu river. It receives the outflow from the Victoria Nile and is drained northward and then westward over the low northern end of the Rift escarpment to Lake Albert.
This lake occupies a very shallow saucer-like depression. The fish fauna of the lake is more akin to Lake Victoria than to Lake Albert. The majority of 46 species recorded are found in Lake Victoria. The lake lacks any large predatory fish except a native species; hence abundance of other small defenceless species. Nile perch was stocked in the late fifties.
There are numerous floating papyrus islands in the lake. In stormy weather, they are blown about the lake. This is hazardous to set nets. Crocodiles were abundant in the lake. Fishermen of surrounding communities practice long line fishing, inshore weed fishing or river fishing with primitive traditional gears.
The lake provides papyrus which is widely used for making mats, roof thatch, fishing floats and rafts. Most of the operational factories around the drainage basin are now defunct hence pollution is not a problem.