Estimates suggest the aquifer could supply the north of the country for 400 years at current rates of consumption.
Scientists say the water is up to 10,000 years old but is cleaner to drink than many modern sources.
However, there are concerns that unauthorised drilling could threaten the new supply.
The 800,000 people who live in the area depend for their drinking water on a 40-year-old canal that brings the scarce resource across the border from Angola.
Over the past decade the Namibian government have been trying to tackle the lack of a sustainable supply in partnership with researchers from Germany and other EU countries.
They have now identified a new aquifer called Ohangwena II, which flows under the boundary between Angola and Namibia.
On the Namibian side of the border it covers an area roughly 70 km by 40 km (43 miles by 25 miles).
According to project manager Martin Quinger, from the German federal institute for geoscience and natural resources (BGR), it's a substantial body of water.