This is a shallow alkaline lake, located, 85 kilometers south-west of Nairobi in a low-lying basin on the floor of the Rift Valley. It covers 10,500 hactares with an Altitude of 580 meters. Its surface is largely covered by crusts of sodium carbonate. Extensive surface water is present only after heavy rains over the local catchment, when run-off reaches the northern end of the lake via three wadis. Most of the lake is a vast expanse of solid sodium carbonate (trona) and allied salts, some 15 - 30 meters thick. This is mined by the Magadi Soda company, whose factory and associated town are on the north-eastern shore. The lake's main basin is 29 kilometers wide and oriented almost due north - south, the northwest arm is 12 kilometers long and 2.5 kilometers wide.

The lake is surrounded and fed with water by a number of hot springs that feed shallow, permanent lagoons at the northern, southern and western extremities (other springs well up invisibly below the surface). These warm lagoons are carpeted with cyanophytes, which are grazed upon by shoals of the fish Oreochromis alcalicus grahami. The climate is inhospitably hotand arid meaning maximum temperatures are 35°C, rainfall c.400 milimeters per year, and the vegetation surrounding the lake is sparse, open bush land.

Bird life is concentrated at the lagoons. Phoenicopterus minor is often present in internationally important numbers though Magadi is a much less significant feeding site for this species than Bogoria or Nakuru. Very large numbers of this species may breed here on rare occasions, perhaps once a century: the last such event was in July 1962, when over a million pairs were nesting. A good variety of other waterbirds is present, including a sizeable resident population of Charadrius pallidus. Mean total water bird numbers in January for between 1994 - 2001 were 25,800. Other birds nesting at Magadi include Platalea alba, Anas capensis, Recurvirostra avocetta and Himantopus himantopus. Many Palearctic migrant waders winter here too, notably Calidris minuta. The bushland around the lake supports 28 of Kenya's 94 Somali - Masai biome species. Casmerodius albus, a regionally threatened species, is an occasional visitor.