Beneath our nation's cities run tens of thousands of kilometres of stormwater pipes, drains and streams. The network of sewers and waterways flows into the ocean, and so does everything that goes down them.

"Stormwater drains end up in creeks, and creeks end up in bays. Dog poo, litter, all end up in streams, and you might be swimming in the bay the next day," said National Institute of Water and Atmospheric Research's chief freshwater scientist, Clive Howard-Williams.

Agriculture is often blamed for New Zealand's declining water quality, but the country's most polluted waterways are found in the inner city.

"I have always thought that city dwellers should be careful about pointing the finger. Before you start moaning at dairy farmers, think about the stream down the road from you," Howard-Williams said.

Many of New Zealand's recreational freshwater ways and coastal beaches failed the water quality pass mark when the Ministry of Environment published its annual report card in October. More than half of monitored rivers were unsafe for swimming and 16 per cent of New Zealand's beaches were rated "poor" or "very poor".

And despite our environmentally conscious image, Kiwis put some strange and toxic things down the drain and their toilets.

As well as hordes of rats and armies of eels, Craig McIlroy, stormwater manager for Auckland, has seen dead cats, dogs and sheep, concrete blocks, tins of paint, nappies and a lot of false teeth wash up in stormwater drains and sewage treatment plants.

"If someone goes home pissed and throws up, he might lose his teeth down the toilet," McIlroy said.

Police have even asked to check the waste water for traces of drugs to trace them to individual homes.

"I am sure a lot of drugs get put down the system," McIlroy said.

"Which means you probably have some eels with some interesting problems."

The biggest issue for cities is chemicals and organic matter being discarded down stormwater drains from individuals and light industry that eventually end up in the sea.

"Paints, poisons and explosives are the things . . . that pollute beaches. At the end of the day a goldfish down the toilet is not going to do any harm," McIlroy said.

Even dog faeces and discarded ice creams contribute to the degradation of waterways and beaches. So does washing the car.

"A lot of that sort of material causes the loss of oxygen, so fish in streams die. There is just too much organic matter and then you end up with bacteria in places where you swim," Howard-Williams said.

Many people believe stormwater is treated before it is fed into the sea, he said. It is not.

"Stormwater drains play a fundamental role in removing floodwater. But the problem is that they end up in creeks, bays and lakes and it is untreated," he said.

City folk needed to appreciate where the stormwater drains end up and be aware of the lengths councils went to keep them clean, he said. "There is a general lack of appreciation of what goes down the stormwater and where it goes. Urban dwellers have a lot to learn."