Cancer drugs are of particular concern because they dissolve easily in water.
The "cytotoxic" drugs, which are used in chemotherapy, are potentially dangerous because they are hard to break down through traditional water purification methods and remain potent in low concentrations.
About 50 of these drugs are prescribed to patients in Britain and researchers are concerned they could be very dangerous if one or more of the drugs mixed together in the water supplies. The drugs make their way into the water system when people prescribed the treatments use the toilet.
Although drinking water in the UK is monitored, none of the cytotoxic drugs are included in the list of contaminants.
The Government has commissioned a pilot project to test river supplies and drinking water after it has been through the water-treatment process, it was reported.
The project has been ordered by the Department for Environment, Food and Rural Affairs (Defra) and the Drinking Water Inspectorate (DWI), which is responsible for overseeing the monitoring of water supplies in Britain.
In January the DWI warned that tap water should be tested after they found traces of bleomycin, a cancer chemotherapy drug, and diazepam, a sedative, in samples of drinking water.
Researchers estimated that an adult drinking more than three pints of water a day would receive a weekly dose of between 300 and 30,000 times lower than recommended safety levels.
Andrew Johnson, a water quality scientist at the Centre for Ecology and Hydrology at Wallingford, Oxfordshire, said: "We have no evidence that these particular drugs are entering the drinking water supply, but we conclude that there is a least the theoretical risk of low-level contamination by cytotoxic drugs.
"It is highly unlikely that concentrations below the nanograms per litre level would represent a risk to adults, however, the developing human embryo inside a pregnant woman could be particularly vulnerable to minute amounts of these agents as they would be able to pass through the gut and placenta."
The testing programme is expected to begin next year at four sites along a major river which yet to be designated. It would continue for at least a year before the results were evaluated