Hundreds of people who recently registered boreholes have admitted using the water they extract for drinking or cooking, raising fears of a possible health risk.
The matter has been referred to the health authorities that are looking into it.
A stock-take of ground water resources carried out late last year by the Malta Resources Authority revealed the existence of about 2,600 boreholes previously unknown to the MRA.
Many of the newly-registered boreholes were found in private residences. The MRA said most of the people using them claimed they drank the water or used it to process food, a practice that could pose a health risk because the water was not professionally tested and treated. It could, for example, have a high concentration of salinity or nitrates, the latter being linked to an increased risk of cancer.
The stock-take formed part of efforts by the authority to crackdown on borehole drilling, particularly as the extraction of groundwater is estimated at about 31 million cubic metres a year, eight million cubic metres above that recommended for sustainable extraction.
A similar exercise carried out in 1997 had revealed the existence of about 6,000 boreholes. The total number of registered boreholes has now risen to 10,000.
Although there has been a reduction in the legal pumping of water from boreholes over the past years, the extraction rate remains unsustainable. Farmers alone are estimated to use 16 million cubic metres a year.
A spokesman for the MRA said it intended to regain the natural characteristics of groundwater as required by the EU Water Framework Directive.
The highest numbers of groundwater sources reported in the last registration exercise were in Siggiewi, with a total of 216, closely followed by 215 in Rabat. Mellieha, Mgarr and St Paul's Bay, including Burmarrad, account for 380.
Some boreholes were found in locations that are highly vulnerable to pollution from dangerous substances, the most common locations being basements, garages, farmyards and public pavements. In these cases, the boreholes will be closed down as they are effectively polluting the surrounding water table and posing a health hazard to nearby users.
The spokesman said the authority planned to ensure a reserve amount for potable needs and a similar reserve to satisfy the irrigation demand by farmers.
"Alternative sources, such as treated sewage effluent and stored surface run-off, will have to be sought if we intend to ensure that those economic sectors that do not require a potable supply of fresh water are adequately sustained in exercising their activities."
Throughout this year, the MRA is imposing a 12-month moratorium on the drilling of boreholes or any form of excavation works in order to be able to analyse the results obtained through the registration exercise. Those who ignore the moratorium by drilling boreholes will be liable to legal action with fines ranging from €20,000 to €50,000.
The MRA is also in the process of drafting regulations for water extraction. Several boreholes, for example, were drilled too deep with negative consequences to the quality of water.