However, data on the Land, Air, Water Aotearoa (LAWA) website - a joint environmental resource launched by authorities last year - showed bacteria levels in the Wairoa River as being "in the best 50 per cent" when compared with other sites nationally.
The sites at McLaren Falls and at the reserve at Ngaumuwahine River, however, carried a "caution" warning as the water quality could at times be "high risk" with a 5 per cent or greater risk of illness.
Health effects from swallowing water tainted with faecal micro-organisms or other bacteria could be unpleasant and include diarrhoea, vomiting and infections.
Meanwhile, the 2013/14 figures collected the Greens showed poor-rated sites in the wider Bay of Plenty included the Rangitaiki River at Thornton Domain; the Ngongotaha Stream at the railway bridge; the Waimana River at the Waimana Gorge Picnic Area; and Puarenga Stream at Whakarewarewa.
The data covered all of the country's monitored rivers except for those in Auckland, Waikato, Northland and the West Coast, where councils did not use SFRG indicators in the period.
Among the worst rated rivers in the data were the Ruamahanga River in Wairarapa, the Manawatu River and the Mangatainoka River - where resident Tui Brewery once portrayed its "Tui girls" frolicking and bathing in blue water.
Nationwide, a total 46 river sites - among them the Wharekopae River at the Rere rockslide, a tourist hotspot near Gisborne - were rated as "very poor".
The Greens claimed there had been a deterioration over recent years, with previous reports from the Ministry for the Environment showing 52 per cent of monitored spots were unsafe for swimming in 2012, compared with 61 per cent in 2013.
"It's quite shocking," the party's water spokesperson 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."
"We are turning ourselves into a country where polluted water is becoming the norm."
Last night, Environment Minister Nick Smith said neither he or 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 dataset" 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 LAWA website that was launched last year and provides an overview of water quality by region.
The LAWA site 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," he said.
"We have increased by five-fold the amount that we are spending on freshwater clean-ups, but we are not going to adopt some of the impractical and rigid rules that the Greens advocate."
