Swimmers are being warned to keep clear of three Whanganui streams - places that are especially popular with young children.
Warning signs went up at the Mowhanau and Kai Iwi streams at Kai Iwi Beach on January 18, and the Ototoka Stream, further north, was deemed unfit for swimming on January 11.
The streams were given "special status" because their poor or highly variable water quality made them unsuitable for swimming, Horizons Regional Council science manager Abby Matthews said.
"Because the results have been consistently poor this season we've made a decision to put permanent warning signage in place for now."
Mowhanau Stream has high levels of E. coli, nitrogen and phosphorous.
E. coli is an indicator of contamination from the faeces of warm-blooded animals. It's usually not a problem in itself, but indicates other disease organisms may be present.
The risk of getting ill depends on the degree of contamination, and that varies over time.
Whanganui Medical Officer of Health Patrick O'Connor said the most likely illnesses from contaminated water were viral.
People swallowing the water can get gastroenteritis and people inhaling it can get acute febrile respiratory illness - a brief fever and cough.
Usually those illnesses will kick in within 24 hours, and people are not obliged to notify health authorities.
"I can't provide you with cases of people that have actually got sick. Even if they did, it's very hard to pinpoint the actual source," Dr O'Connor said.
The exception would be a whole group of people, who had been doing the same thing, getting sick at the same time.
"It's almost impossible to make conclusions from individual cases."
Despite any evidence of real risk, the warning signs were worthwhile, he said.
"I don't think it's alarmist. It's giving people the best information that we have. We've got to share that information. Clearly people will make their own decisions as a result of that."
He said there could be other coastal streams affected.
"They don't obviously monitor every coastal site. There may be more widespread problems."
Horizons monitors more than 80 swim spots weekly during the summer months. On Thursday there was a contractor taking monthly water samples in the Mowhanau Stream where the council has been working to improve water quality.
Ms Matthews said: "We are looking into further investigative work to determine the cause(s) and identify any opportunities for improvement.
"We appreciate this is a popular spot with families and that the community are keen to be able to make good use of it."