Otjikoto is situated close to the mining town of Tsumeb. Part of an underground river system, the lake was exposed when the roof of what was a large dolomite cave fell in. The lake is small with a diameter of about 102m, but very deep, with a depth estimated to be in excess of 142m in places. The lake is situated near the town of Tsumeb and is en-route from there to the Namutoni entrance to the Etosha National Park.

During the first world war the Union of South Africa, still part of the British Empire, was ordered to invade German South West Africa. The German troops were heavily out-numbered by the Union forces, but managed to hold out for nearly a year before finally being forced to surrender. The final hostilities took place in the vicinity of Otjikoto and, rather than surrender their weapons and artillery to the enemy everything, including the heavy guns and ammunition wagons, was dumped into the lake. Many of these relics have since been recovered, but not all. The lake still contains various pieces of artillery and there are rumours that the German troops also disposed of their war chest in the same manner. Stories are told of a large safe, the edges and keyhole sealed with molten lead and containing 6 million goldmarks, being lowered into Lake Otjikoto. The safe has never been seen again.

The first Europeans to see Otjikoto were the Englishman Sir Francis Galton and the Swede Charles Anderson who discovered the lake by accident in 1850.

The name is derived from the Otjiherero language and means deep hole. The San called it "Gaisis" which means very ugly because they were afraid of the deep water. When Galton and Anderson first stumbled on Otjikoto they went for a swim. The local Herero and Owambo people were much surprised because local belief was that nobody could survive the mysterious waters.

Lake Guinas, is situated southwest of Otjikoto, a 50km (31miles) round trip from the main road, but it is usually bypassed in favour of Otjikoto. The detour is well worth the effort, as Guinas is not only deeper, but more scenic than its more famous counterpart.