Sewage which entered an Ahuriri waterway contributed to the prolonged closure of the nearby Pandora Pond, now in its fourth week.
The popular water spot has been closed since February 21, after a high reading of 475 Enterococci per 100ml. The safe swimming guideline is 280.
Just over a week later around March 4, sewage is believed to have entered Napier Marina's inner harbour because of a blockage in the sewer system in Meeanee Quay.
The "inner harbour" is defined as the fishing boat side of Meeanee Quay, from Westshore Bridge to the harbour mouth, by the Hawke's Bay Regional Council.
Napier City Council manager asset strategy Chris Dolley said the blockage on Thames St was caused by gravel and sand.
Wastewater backed up and entered the roading stormwater network though a lifting eye in a manhole near Westshore Bridge.
"At the incident site, it was the view of the operators that no wastewater had entered the inner harbour although it's difficult to be certain," he said.
Sampling by the regional council confirmed the discharge reached the inner harbour after entering the roadside stormwater drain, which drains into the inner harbour.
Regional council manager resource use Wayne Wright said the quantity of sewage that reached the inner harbour was unknown, but "enough entered the waterway to exceed acceptable limits as per the sample results".
The discharge was discovered by regional council staff on Sunday, March 4. After being advised, Napier City Council staff attended "straight away" to clean the remains of the discharge, the roadside sumps and gutters, and removed the blockage.
Mr Wright said the council was unable to comment further because enforcement action was pending.
In the week after the closure, Hawke's Bay Regional Council reported samples from Pandora Pond were clear.
When asked if this contributed to the pond's prolonged closure, a Hawke's Bay District Health Board spokesperson said: "We were aware of the possibility of sewage going into the harbour from this event, and given this information it was prudent to keep the swim warning in place.
"We are awaiting further information from Napier City Council and Hawke's Bay Regional Council to understand this event and its implications.
"The swim warning will remain in place with results continuing to show elevated results of contamination."
After heavy rainfall last week levels soared to 770 Enterococci per 100ml. This is the second time in a year sewage has entered the water in this area.
Last April, heavy rainfall brought by Cyclone Debbie overwhelmed Napier's sewerage system, leading the city council to discharge 2.5 million litres of wastewater into the Ahuriri Estuary to keep streets safe from overflow.