Almost all of New Zealand's lowland streams and rivers are unsafe to swim in.

A damning report by the National Institute of Water and Atmospheric Research on 229 lowland waterways has found that New Zealand's clean, green self-image is no longer true for our water.

Almost 95 per cent of the lowland streams and rivers have levels of faecal bacteria that exceed Ministry of Health guidelines.


Half have levels that are more than five times the guideline.

Almost all the waterways in lowland areas of the North Island, including the Waihou, Piako, Waipa, Whanganui and Manawatu Rivers, show up in the study as at risk of failing the health guidelines.

A notable exception is the Waikato River, which "potentially meets the guideline" above Mercer.

Most Bay of Plenty rivers such as the Rangitaiki and Whakatane also potentially meet the guideline above their lower reaches.

Waikato Medical Officer of Health Dr Dell Hood, who has spoken out about the problem before, said the study showed children should not swim in most of the country's lowland rivers, and certainly should not put their heads under the water.

"We have to say to people that any exposure to this sort of level of bacteria increases your chances of getting gastrointestinal illness.

"That would be very unpleasant but for healthy children it would not be life-threatening. You would, however, be very unwise to let toddlers in water like that."

But it was still safe to swim and drink in the bush-clad upper reaches of rivers and streams that were not polluted by cities or livestock.

The study, published in the New Zealand Journal of Marine and Freshwater Research, is the first time data from all regions has been brought together.

The head of Niwa's National Centre for Water Resources, Ton Snelder, said the recommended guidelines were quite harsh criteria for water quality, but appropriate for rivers used for swimming.

"What is surprising and perhaps a little alarming to people is that these numbers correspond with such a significant proportion of the total New Zealand rivers."

Auckland Regional Council freshwater ecologist John Maxted said the most surprising finding was that bacteria levels in streams and rivers in farming areas were as bad as in city streams.

Levels of phosphorous and nitrogen in streams in farming areas increased from 1996 to 2002 because of more intensive farming, especially dairying.

But levels of ammonia and other industrial pollutants dropped and, after allowing for changes in weather patterns, there was no worsening in water clarity or temperature.

A Ministry for the Environment official in charge of sustainable water development, Elizabeth Eastmure, said the ministry would issue discussion papers in the next three months seeking public input on water policy, including options for managing livestock effluent such as fencing off streams and planting trees beside them.

A Tourism New Zealand spokeswoman said the report would not stop the agency from marketing the country as "100 per cent pure".

"The 100 per cent Pure New Zealand campaign markets the unique experiences New Zealand offers. For example, a hongi is a 100 per cent Pure New Zealand experience - one that you could not have anywhere else in the world," she said.

"Our natural environment is one of the elements of the unique experience and what New Zealand is best known for. Our research shows that the main reason visitors come to New Zealand is because of its stunning landscapes and natural environment."

Fish and Game Auckland/Waikato manager Doug Emmett said the report was no surprise to his organisation, which ran a campaign against "dirty dairying" last year.

The campaign helped to push Fonterra into signing an accord with the Government to assess all its dairy farmers against a number of environmental standards. But Mr Emmett said there was still a long way to go.

"We talk about New Zealand being 100 per cent pure. I think 50 per cent pure is stretching it a bit, quite frankly," he said.

Dr Hood said the study showed that society was finally taking water quality seriously.

The report: