Generally stored at depths of more than 250 metres (820 feet) under the Earth's surface, the ancient resource had been assumed to be shielded from pollution by humans - who rely on it more and more as shallower sources dry up.
Now, researchers have found traces of modern-era rainwater in wells that bring "fossil" groundwater to the surface - pointing to a contamination risk.
"It's a bit like going to an old folks' home and suddenly realising there are also little kids running around. That's great, except if the little kids have the flu," said study co-author James Kirchner of the Swiss Federal Institute of Technology in Zurich.
The fear, he explained, is that younger water may pollute the ancient aquifers with fertilisers, pesticides or industrial runoff from Earth's surface - though they have not found any evidence for this yet. Groundwater is rain or melted ice that filters through Earth's rocky layers to pool in aquifers - a process that can take thousands, even millions, of years. It is the largest store of unfrozen fresh water on Earth. Groundwater is pumped to the surface with wells for drinking and irrigation, and supplies about a third of human water needs.