Last year's Government "report card" on rivers found half those assessed were unsafe to swim in.
Sad news for nostalgic Kiwis recalling the pristine swimming spots of youth, this study also highlighted the plight of animals attempting to live in this country's increasingly polluted waterways.
Massey University freshwater ecologist Mike Joy says pollution, plus habitat loss, construction of dams and other barriers and over-fishing have decimated native fish.
"Our largest freshwater predator, the longfin eel (females can reach 2m) is in trouble," he says.
The other main native eel species, the shortfin, copes far better with murky polluted rivers, lakes and wetlands. The longfin prefers clear upland rivers and streams. Dams and other barriers interrupt its complex life-cycle. Males are ready to breed at about 25 years old but females are not ready till 40 year or older. Once mature, they attempt to swim downstream and out to the sea, heading to the tropical Pacific between New Caledonia and Fiji.
After spawning, adults die while the hatchlings (elvers) ride the ocean currents home and attempt to swim up rivers their parents came from. But as well as being stymied by dams and other barriers, eels are heavily fished by iwi, recreational and commercial fishers.
Kiwi eel meat is snapped up in Asian countries where native stocks have dwindled.
Last year Parliamentary Commissioner for the Environment, Dr Jan Wright, called for suspension of commercial fishing until longfin stocks are shown to have recovered. She also recommended an international review by an expert panel, which the Ministry of Primary Industries commissioned late last year. The panel criticised the limited set of scientific information and recommended a more comprehensive approach be taken.
So how much trouble is the longfin eel in?
Dr Wright's report surveyed all the available evidence and concluded that longfin eels are in serious trouble. She says longfin eel numbers may be 20 per cent, or less, what they were in the early 20th Century.
Her report painted a grim picture of eels being prevented from making their way up and down rivers. This applied both on their once-in-a-lifetime trip to the sea to spawn and as tiny elvers seeking to swim upstream to upland rivers. Irrigation pumps and structures such as dams and weirs effectively block the way in both directions, and these blockages - plus over-fishing - have already caused some localised populations to go extinct.
Dr Wright's report said a moratorium on commercial harvesting would be the fastest way to protect the resource while further data is gathered.
However, the tone of the independent panel's report seemed far more guarded. For example, the panel found only "a high probability" that the longfin eel population had been substantially reduced relative to its pristine numbers.
Dr Wright was disappointed that the panel could not make firm conclusions about the status of the longfin eel.
"I think this may be because of the limited time available, and through no fault of the panel members," she said.
Iwi hold quota
Her report criticised the Ministry for not having set a target for the longfin eel population to ensure it is rebuilt, something the Ministry of Primary Industry has now committed to doing.
She called for South Island longfin and shortfin limits to be separated so the limits for longfin eel could be reduced without affecting the limits for shortfins.
The Ministry of Primary Industries has also since agreed to review catch limits to rebuild stocks, and will consider separating the South Island allowable catches. Dr Wright said she found these steps encouraging.
"Under the Fisheries Act, the Minister has to go through a process to do this (review the catch limits), Dr Wright points out.
"The Ministry has to do the science, put forward options and consult, so it does take time. There is something happening there.
"Separating out the South Island quota may also take time; South Island iwi and quota holders need to be consulted. The split was anticipated when the eels were first bought into the quota management system, and the 1997 Ngai Tahu Settlement records that the two should be managed separately where practicable."
Largest in the world
The longfin eels breed only once - at the end of an extraordinary lifecycle.
They begin their lives in the tropical Pacific Ocean. Eggs hatch into larvae shaped like leaves and drift on ocean currents all way to New Zealand - the only country where they are found.
Close to land, they turn into glass eels and swim into estuaries and river mouths. These glass eels become elvers and migrate up rivers in shoals for 2 or 3 years until they find somewhere to live. There they can grow to over 2 metres long and over 20 kg - the biggest and longest lived eel in the world.
After decades - about 40 years for females, and sometimes more than a century - they get the urge to breed. When ready, the eel transforms: Its eyes turn blue and bulgey, its head becomes streamlined, its stomach shrinks, and its belly turns silver.
Swimming down rivers with the autumn rains and out to sea, they begin a 5,000 km journey back to where their life began. There they breed once and die.
"This long slow lifecycle, and single opportunity to breed, makes them very vulnerable. It is crucial to understanding why the eel is in trouble and what we need to do about it."
Adapted from the Parliamentary Commissioner for the Environment's 2013 report