Researchers have found significant levels of prescription drugs in water samples from Sydney Harbour.

Samples of the drugs were found in an analysis of samples of marine water from 30 sites, which were located close to stormwater outlets across the entire Sydney estuary.

The evidence included traces of strong painkillers, anti-depressants, beta blockers and epilepsy medication.

Water scientist Gavin Birch from the University of Sydney’s School of Geosciences says it is the first time this kind of research has been undertaken in Australia.

"I was surprised how widespread the drugs were in the samples. Paracetamol was found in all 30 sites, whereas one particular artificial sweetener was found in 27 sites," he told reporters.

"The presence of acesulfame [a marker of domestic wastewater] and pharmaceuticals in water from all parts of the estuary after a dry period, suggests sewage water is leaking into the stormwater system in this catchment," he said.

Luckily for swimmers, the levels of the drugs in Sydney Harbour waters were in low concentrations, though the potential for harm is not entirely understood.

"When this has happened in other areas, it certainly has had an impact on the fish and environment," Mr Birch said.

Researchers said sewage water should only be discharged to the estuary when it overflowed during heavy rainfall.

Seven pesticides were detected too; 2,4-dichlorophenoxyacetic acid, 3,4-dichloroaniline, carbaryl, diuron, 2-methyl-4-chlorophenoxyacetic acid, mecoprop and simazine.

"The pesticides are applied to the environment and were discharged via stormwater to the estuary," the researchers said.

The study also sought evidence of a range of antibiotics and personal care products, but none were found.