The new aquifer – called Ohangwena II – flows under the border between Angola and Namibia, covering an area of about 43 miles by 25 miles on Namibia's side.
The water is up to 10,000 years old and cleaner to drink than many modern sources.
Project manager Martin Quinger told BBC that the stored water could last 400 years based on current rates of consumption.
Currently the 800,000 people living in the northern part of the country get their drinking water from a 40-year-old canal that brings the scarce resource from Angola.
Quinger added that Ohangwena II could change the nature of farming in the area, which has only been viable near two rivers in the region, and could act as a natural buffer for up to 15 years of drought.
Natural pressure will make the water easy and cheap to extract.