The WA Health Department is warning against eating fish or crabs from the Swan River after potentially toxic microscopic algae was detected at elevated levels.

Potentially toxic microscopic algae has been detected at elevated levels in Perth's Swan River, prompting the West Australian Health Department to advise against eating fish, crabs or shellfish collected from the water.

The warning extends from the Old Swan Brewery to the Garrett Road Bridge, including Perth Waters, Elizabeth Quay, Barrack Street Jetty and Claisebrook Cove.

Acting environmental health executive director Michael Lindsay said ingesting toxins produced by the microscopic algae could cause paralytic shellfish poisoning.

"These algae, which are not visible to the naked eye, can produce a toxin which could be absorbed by filter feeding shellfish and potentially consumed by crabs and finfish to a lesser extent," he said on Wednesday.

"Cooking will not destroy these toxins."