Lake Naivasha is at the highest elevation of the Kenyan Rift valley at 1,884 metres. 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.

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The lake had a normal surface area of 139 square kilometers before 2010 and had increased to 198 square kilometres by 2020. It is surrounded by a swamp which covers an area of 64 square kilometres, but this can vary largely depending on rainfall. Situated at an altitude of 1,884 meters the lake has an average depth of 6 meters, with the deepest area being at Crescent Island, with a maximum depth of 30 meters. Njorowa Gorge once formed the lake's outlet, but it is now high above the lake and forms the entrance to Hell's Gate National Park.

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The lake is home to a variety of types of wildlife including over 400 different species of bird and a sizable population of hippos. The fish community in the lake has been highly variable over time, influenced by changes in climate, fishing effort and the introduction of invasive species. The most recent shift in the fish population followed the accidental introduction of common carp in 2001. Nine years later, in 2010, common carp accounted for over 90% of the mass of fish caught in the lake.

There are two smaller lakes in the vicinity of Lake Naivasha: Lake Oloiden and Lake Sonachi (a green crater lake). The Crater Lake Game Sanctuary lies nearby.