Authorities have discovered harmful bacteria at a children's water playground at Perth's new Elizabeth Quay.

The discovery means the water park has been shut for a second time.

WA Department of Health workers say the bacteria in the water spray and amoeba in the park's waste pipes were picked up during routine sampling.

“In the interest of public safety, and following best practice guidelines, the BHP Billiton Water Park was closed to allow for modifications to the park's filtration systems,” Chief Health Officer Tarun Weeramanthri said in a statement.

“While tests are needed to confirm if the amoeba is pathogenic [disease-causing], the presence of pseudomonas bacteria can cause skin rashes or ear or eye infections in some people.

“Anyone who experiences these conditions following exposure to the water park should visit their GP.”

It comes less than three weeks after the park had be switched off due to an amoebae outbreak, but the Health Department insists it was treated appropriately at the time.

The park opened for the first time in late January this year, but there has been no word on when it will be reopened this time.