The Hervey Bay Hospital is disinfecting its water system after it tested positive to legionella bacteria.

A Queensland hospital is flushing and disinfecting its water supply after detecting legionella bacteria in the system.

Patients at the Hervey Bay Hospital must now only drink bottled water and avoid showers as the facility tries to eradicate the bacterial strain.

The moves come after a patient who died at the facility in April tested positive to legionella.

The deceased patient's cause of death was still being investigated, Wide Bay Hospital and Health Service chief executive Adrian Pennington said.

"We have a rigorous testing process of our water in hospitals and when we have a positive result we err on the side of caution," he said.

Other measures to avoid an outbreak include not using tap water during invasive procedures.

Public and environmental health workers, as well as hospital maintenance staff, will continue testing supply sites at the hospital on Thursday.