Lake Tanganyika is the deepest of the Rift Valley Lakes of Central/East Africa, with a maximum depth of about 1,470m. It has an area of around 34,000km2 and is estimated to be about 10–15 million years old. The surface layers of water are a tropical 24–28°C and support virtually all of the known life in the lake.

Well below these, where it is too deep for the sun's light to reach, are separate, colder waters. Below about 200m, these are deprived of oxygen and hardly mix with the upper layers. They are currently the subject of much scientific study.

The lake has a variety of habitats around its 3,000km-or-so of shoreline, ranging from flat sands to marshy areas and boulder-strewn shores. Most of the fish species live within about 30m of the surface, where the water is generally very clean and clear, with a visibility as high as 10–20m in places.