Lake Kyoga is about 1,720 km2  in area and at an elevation of 1,033 metres.  The Victoria Nile flows through the lake on its way from Lake Victoria to Lake Albert. The main inflow is from Lake Victoria at the Source of the Nile river in Jinja. Another source of water is the Mount Elgon region. Lake Kyoga is part of the Great Lakes system.

The lake reaches a depth of about 5.7 metres, and most of it is less than 4 metres deep. Much of the swampy shoreline is covered with papyrus and water hyacinth. The papyrus also forms floating islands that drift between a number of small permanent islands. Extensive wetlands fed by a complex system of streams and rivers surround the lakes. The extensions of the lake include Lake Kwania, Lake Bugondo, and Lake Opeta.

Forty-six species of fish including Nile Perch that was introduced in 1950s have been found in Lake Kyoga, and crocodiles are numerous.