A statement said Hawke's Bay Regional Council science staff were investigating the source of the faecal contaminants at Opoutama.
It said factors other than rainfall may also have contributed to the contamination and other sites in the area were being resampled until results were clear.
The public should avoid swimming at the Mahia sites until further notice.
Previous warning for other Hawke's Bay swimming areas were no longer in place.
Wairoa District Council chief executive Peter Freeman said the high faecal bacteria readings in the Mahia area were a regular occurrence after heavy rain.
"That's why we are spending $13 million," Mr Freeman said.
The Opoutama roading and wastewater project infrastructure was in place and the Mahia scheme was currently being commissioned.
"If there is no change to the faecal contamination after spending all of this money, we will be severely disappointed," he said.
Both schemes went to the Environment Court following community opposition.