The journal Proceedings of the National Academy of Sciences also said 44 per cent of the wells contain dangerously high levels of manganese which interferes with the development of growing children.
"About 7 million people are at a considerable risk of chronic arsenic poisoning. This is particularly worrying because groundwater is the main source of drinking water throughout the delta," lead author Michael Berg told Reuters news agency.
The delta, which straddles eight provinces and travels through the capital Hanoi and Hai Phong port, is home to nearly 17 million people.
Eleven million people have no access to the municipal water supply and are dependent on other sources, such as tubewells.
"Sixty-five per cent of the wells contain naturally occuring toxic elements, at levels which exceed the World Health Organisation's safety standards," Berg added.
It is believed that the widespread contamination is due to a long history of groundwater exploitation in the delta.