Lake Naivasha is at the highest elevation of the Kenyan Rift valley at 1,884 meters (6,181 ft) in a complex geological combination of volcanic rocks and sedimentary deposits from a larger Pleistocene era lake. Apart from transient streams, the lake is fed by the perennial Malewa and Gilgil rivers. There is no visible outlet, but since the lake water is relatively fresh it is assumed to have an underground outflow.

The lake has a surface area of 139 km² and is surrounded by a swamp that covers an area of 64 square km, but this can vary largely depending on rainfall. It is situated at an altitude of 1,884 meters (6,180 ft). The lake has an average depth of 6 m (20 ft), with the deepest area being at Crescent Island, at a maximum depth of 30 m (100 ft). Njorowa Gorge used to form the lake’s outlet, but it is now high above the lake and forms the entrance to Hell’s Gate National Park. The town of Naivasha (formerly East Nakuru) lies on the northeast edge of the lake.