Drought conditions are triggering problems for sewerage systems in the Far North with problems at Kaitaia, and Doubtless Bay.
The Far North District Council says it will be forced to release treated effluent into Kaitaia's Awanui River next week, despite an order not to.
The Northland Regional Council has forbidden the council to discharge from its Kaitaia sewage ponds, because of low river levels.
But council spokesperson Alison Lees says the ponds have only a week's storage left in them.
Ms Lees says the Far North council can see no alternative but to discharge, despite the regional council's directive.
She says to make matters worse, the Kaitaia sewerage ponds are now infected with an algae that is hard to eradicate, and could be toxic to people and stock downstream.
The prolonged humid weather has also caused a toxic algal bloom in sewage ponds at Taipa, in Doubtless Bay.
The Far North council stopped discharging treated water last week because of the bloom, but the ponds are now full to the brim and it says it has no choice but to release the water.
The council says the ponds have been treated to kill the algae, but the discharge could still be toxic.
It has put up signs at Taipa warning against swimming and gathering shellfish.