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The team carried out the first continentwide analysis of underground water-permeable rocks and established that around 30 times the amount of water that falls as rain in Africa each year lies largely untouched underground.
The greatest groundwater storage they found was in North Africa, specifically Libya, Algeria and Chad, where large sedimentary basins were filled around 5,000 years ago when the climate was wetter.
The scientists – from the British Geological Survey and University College London – believe that with careful management, the water supply in the aquifers could keep Africa going for generations, even factoring in the vagaries of climate change.
At present, around 300 million people across Africa do not have access to safe drinking water. The continent's population is also growing – the latest UN figures suggest it will double over the next four decades to almost two billion, putting further pressure on water supplies which are also needed to grow more food.
Experts have cited a global scarcity of water and rises in food prices as the likely causes of the world's biggest future conflicts.
Dr Alan MacDonald, of the BGS and lead author of the study, said they hoped the mapping would reduce "scaremongering" about the state of water supplies in Africa and allow its citizens to make more informed choices.
"What we have found is that for many of those 300 million people going without clean water, it's not that the water resources are not there, it's for other reasons," he said.
"Many of those people live in areas where the aquifers are constantly being recharged by rainfall and if they were given access to a borehole with a hand pump, those water supplies would be sustainable as drinking water." But he cautioned against the widespread drilling of large boreholes to use for plant irrigation.
"That would take up to 100 times as much water as the use of hand pumps and could cause a diminishing of supply," he said.
The study of Africa's groundwater supplies was funded by the Department for International Development and first published in the Environmental Research Letters journal.