People in Napier are being warned to avoid all contact with water from the Ahuriri estuary, due to concerns over E-coli.
The Hawke's Bay Regional Council said heavy rain and wastewater discharge into the estuary last week have contaminated it with high levels of E-coli.
The District Health Board said people should not swim or collect shellfish for eating from the area.
Medical Officer of Health Dr Nick Jones said confirmation of E-coli meant swimming and water based activities in contaminated water posed a risk of infections of the stomach, skin, eyes and ears.
He said gathering shellfish was never recommended from Ahuriri, but with flows of wastewater into the estuary, risks were likely to be even higher than normal for some time, because shellfish could take several weeks to clear any contaminants they absorbed.
"While the wastewater overflow does not appear to have affected other swimming locations, heavy rain tends to be associated with increased risks from swimming due to run-off generally. Standard advice to avoid swimming in all fresh waterways such as lagoons, streams, and rivers for at least three days after heavy rain should be followed," he said.