The aquifer could bolster development in Namibia with the water thought to be cleaner to drink than many of its alternative sources.
Scientists say the water is up to 10,000 years old and the amount stored in the new source is enough to cater for north Namibia for 400 years, the BBC News reported.
"The amount of stored water would equal the current supply of this area in northern Namibia for 400 years, which has about 40 percent of the nation's population, " said the BBC project manager Martin Quinger, from the German federal institute for geoscience and natural resources (BGR), said.
"What we can say is that the huge amount of stored water will always be enough for a back up for an area that is currently supplied only by surface water," Quinger said.
"If the water [has spent] 10,000 years underground, it means it was recharged at a time when environmental pollution was not yet an issue, so on average it can be a lot better than water that infiltrates in cycles of months or years," he said.
The Namibian government has long been trying to deal with the issue by calling in supplies from countries across Europe but have now identified the new aquifer, called Ohangwena II, which flows under the boundary between Angola and Namibia.
The major issue now facing the area, however, is those looking to exploit the new source and look to carry out illegal use.
Namibia has more than 300 days of sunshine per year and average in some coastal areas have an average rainfall of zero, with droughts inevitable, meaning others will possibly look to take advantage of the source.