Farm run-off and dodgy sewage tanks have made many Bay of Plenty rivers unsafe to swim in, according to a government report card.
The latest recreational water quality report from the Ministry for the Environment shows most of New Zealand's favourite monitored fresh water swimming spots are a health risk and should be avoided.
Bay of Plenty Regional Council water science manager Rob Donald said the lower water quality reflected the land use.
"Anywhere where there's farm activity near a bathing site you can generally expect there to be a higher risk, whereas if you look at the open coastal sites in the Bay of Plenty - they are of very good water quality."
The ministry assessed the country's 210 freshwater beaches and 248 coastal beaches used for recreation, based on monitoring data acquired over five consecutive summers.
The beaches were given one of five grades to describe their likely condition for recreation during the summer, based on an assessment of potential sources of faecal contamination.
The grades ranged from very good - considered satisfactory for swimming at all times - to very poor, representing a high risk of illness and should be avoided.
Faster rivers fared better, Mr Donald said.
"Generally, the faster the river flow, the faster waterways will recover from contamination - they clean themselves out."
Some of the larger waterways fared better improving the quality of direct sewage discharges, Mr Donald said.
"The Tarawera River was a good example where the Kawerau town sewage was removed from the river. We had quite a dramatic improvement in the quality of the river because of that."
Repairing and maintaining sewage tanks in the area was also helping to restore the waterways, Mr Donald said.
Senior Massey University ecology lecturer Mike Joy said the results weren't surprising.
The clear differences between the good and the bad sites were whether they were upland or lowland, he said.
"When I look at the local sites I know of - swimming holes like Horseshoe Bend on the Tokomaru River - it comes straight out of native forest and there's a lovely swimming hole and it's beautiful and of course there's no E. coli, there's no problem with bacteria.
"If you look at any of the sites downstream they fail because of all of the run-off from dairy farms and the effluent from the wastewater treatment plants."
The report highlighted the effects of uncontrolled intensification of dairy farming and a complete failure to protect fresh water, Dr Joy said.
Stronger legislation, fencing cattle off from waterways and riparian planting is needed to help protect fresh water from further contamination, Dr Joy said.
A new member's bill drafted by Green MP Catherine Delahunty aims to tighten controls on sustained pollution of waterways. It would close a loophole in the Resource Management Act that allows contaminating discharges with toxic effects and discoloration of waters under "exceptional circumstances".
Ms Delahunty said the current phrase had no timeframe and her bill would limit its use to five years.
The most "legendary example" was the Tarawera River in Bay of Plenty that inspired the "Black Drain Bill", she said.