Only 20 per cent of monitored river recreation sites were graded good or very good.
Health effects from swallowing water tainted with faecal micro-organisms or other bacteria can be unpleasant. They include diarrhoea or vomiting, and infections of the eye, ear, nose and throat.
Children were particularly at risk of ear and skin infections, said the medical officer of health with the Toi Te Ora Public Health Service, Dr Phil Shoemack.
The report card canvassed sampling from 210 freshwater beaches, including lakeside areas, and 248 coastal beaches used for recreation that had been assigned grades based on monitoring data acquired over five summers.
Coastal beaches and freshwater beaches at lakes were found to be much cleaner than river sites.
Eighteen per cent of coastal beaches were graded as "very good" and a further 42 per cent as good.
Northland, Taranaki, Southland, Bay of Plenty and Marlborough were the worst regions for river quality at monitored recreational sites, although results from Auckland, Waikato and some other areas were not included.
A ministry official said the sites were chosen for their susceptibility to risk factors that might make swimmers sick, as well as their popularity for recreation, and were not representative of the overall water quality in the country's swimming spots.
Green Party environment spokeswoman Eugenie Sage said the results fell far short of what Kiwis should expect.
"It shows what a fake marketing image 100 per cent pure is, and we need to take action to make that image real," she said.
"By undermining the credibility of the brand, people will wake up to that internationally and see there's a major gap between the marketing image and reality.
"We need strong rules and water quality standards to clean up our rivers and prevent faecal contamination from agricultural intensification."
Environment Minister Amy Adams said our water quality was good by international standards and most popular sites were fine for swimming.
But she didn't see that as good enough, saying: "My preference will always be for all our sites to be safe for swimming."
