A total of 46 river sites - among them the Wharekopae River at the Rere rockslide, a tourist hotspot near Gisborne - were rated as "very poor".
Health effects from swallowing water tainted with faecal micro-organisms or other bacteria could include diarrhoea, vomiting and infections.
A further sixty-three sites - including two popular swimming spots in the Wairoa River near Tauranga - ranked as poor.
The Greens claimed there had been a deterioration over recent years, with reports from the Ministry for the Environment showing 61 per cent of monitored spots were unsafe for swimming in 2013, compared with 52 per cent in 2012.
"It's quite shocking," the party's water spokeswoman, Catherine Delahunty, said.
"Families should be able to head down to their local swimming hole and jump right in the water without worrying about getting sick."
Last night, Environment Minister Nick Smith said neither he nor the ministry had been able to properly assess the figures, but felt they should be treated with caution.
"Just comparing the results from one year after another does not give a long-term trend on freshwater quality."
Dr Smith also felt it would be "false" to draw conclusions around the country's overall freshwater quality from what he considered a "narrow data set" that wasn't representative of all freshwater bodies.
The ministry had advised him that while New Zealand's freshwater quality matched up well by international comparisons, there had been "increased pressure" on lowland areas.
The ministry hasn't released a national report card since 2013, but it has collaborated on the Land, Air, Water Aotearoa (LAWA) website that was launched last year and provides an overview of water quality by region.
The LAWA website showed median river bacteria (E.coli) levels in the Auckland region were in "the worst 25 per cent" of sites in the country, while Waikato's median bacteria levels were in the worst 50 per cent.
Ms Delahunty described the Government's national standards for freshwater - introduced last year and requiring a minimum standard to make rivers safe for "wading" and boating, and allowing local authorities to set higher standards if they wanted - as "weak" and a "licence to pollute".
Measures proposed by the Greens include rules that ensure rivers were clean enough to swim in and fenced livestock out of waterways, an extra $20 million each year for a decade for sewage treatment upgrades in small towns, and a "resource rental charge" for irrigation.
But Dr Smith dismissed the Greens' policies as "simplistic", adding they would block a number of significant water quality schemes.
"The Government is determined to drive a programme that will see improved management and standards of freshwater quality."
New Zealand's top freshwater ecologists have met in Palmerston North this week to thrash out a simple way to assess the state of our river habitats.
Scientists from Massey, Auckland, Canterbury and Waikato universities have teamed up with experts from NIWA, the Government and regional councils to establish measures where river habitats could be defined as pristine, good, impacted or degraded.
Their ultimate goal is to achieve better management of rivers and halt or revert damage already done.
With around 39 per cent of native freshwater fish considered threatened, Massey ecologist Dr Russell Death said it was critical that new policy and planning regulations were informed by the best research.
"We know a lot about river habitats, but to come up with a single index to able to be used in resource consents is what we are trying to work our way through."
It was hoped what came out of the two-day workshop would be incorporated into a Government review of the National Objectives Framework for rivers next year.
