Problems have been detected with the filtration membranes at Motueka's Wastewater plant, and warnings issued against collecting shellfish or whitebait.
Tasman District Council engineers have noticed the final membranes in the filtration system are degraded, and not working as expected.
Water supply and wastewater team leader Becky Marsay said staff did not know what had caused the issue, and were urgently investigating a fix.
The membranes remove any remaining bacteria and minute particles before the water is discharged from the processing plant.
Marsay said it was likely the membranes would need to be replaced, but sourcing new ones and having them installed could take several months.
The council has reverted to using an older system, where partially treated wastewater is pumped into an adjacent soakage area and filtered through the ground.
This treatment method was retired several years ago but was being used again to avoid uncontrolled wastewater overflows.
As a precaution, people are advised not to take shellfish or whitebait from the area until further notice.