Hawke's Bay District Health Board is warning the public not to swim, collect shellfish for eating or partake in any other water based activities in the Ahuriri Estuary.
The Napier City Council made the decision to divert part of Napier's waste water network into a storm water drain that flows in the estuary to save the streets from sewerage overflow.
The diversion has already stopped and Hawke's Bay Regional Council pollution staff are now water sampling in the area.
Medical Officer of Health Dr Nicholas Jones said levels of bacteria and viruses were likely to be higher in the estuary and people should avoid any recreational water activities in this area until sampling shows levels are safe.
"Swimming in contaminated water poses a risk of infections of the stomach, skin, eyes and ears."
Dr Jones said the gathering of shellfish is never recommended from Ahuriri but with flows of waste water into the estuary risks were likely to be even higher than normal for some time.
"This is because shellfish can take several weeks to clear any contaminants they absorb."
"While the waste water 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."
