The Irwell River near where it flows into Lake Ellesmere.

The Irwell River would swell with anglers on Friday nights, combing the darkened river until the sun came up. Now the water is green and the fish have long gone.

It is one of the many polluted waterways flowing into Canterbury's Lake Ellesmere, one of the country's most ecologically important lakes - yet one of its most polluted.

It highlights the mammoth challenge that will be the lake's restoration, likely New Zealand's largest freshwater clean-up project.

JOHN KIRK-ANDERSON/FAIRFAX NZ The water is a deep green colour.

About 40 rivers, streams and drains flow into the lake, filling it with the sediment and nutrients that made it eutrophic.

READ MORE:

* Health board warns against contact with 10 Canterbury waterways

* Warnings over four South Canterbury waterways

* Risk of more waterway problems after Port Hills fires

* No longer swimmable: A community mourns its lost river

* Is this Christchurch's most plastic-polluted beach?

Many of those spring-fed waterways have become severely polluted, primarily because of land-use intensification in the district.

DAVID WALKER/FAIRFAX NZ The Selwyn River near the lower Selwyn Huts in January.

For those who once used the Ellesmere fishery, considered one of the finest in New Zealand, the decline over two decades grated.

Rivers such as the Irwell and the Selwyn went from hosting thousands of fish to virtually none - no longer swimmable or worth fishing.

"The Irwell was a beautiful fishing river, just a lovely river," said John Kent, a retired GP who has had a fishing licence for nearly 70 years.

CHARLIE MITCHELL/FAIRFAX NZ Boggy Creek where it flows into Lake Ellesmere.

"That's what really prompted me to get involved into the conservation of water, seeing what happened at the Irwell. I just couldn't believe it."

Kent has fished hundreds of the South Island's rivers - he wrote the award-winning South Island Trout Fishing Guide.

He recalled picnics by the Irwell with his mother - sitting on its banks, a fishing rod in one hand to catch trout. Nowadays, the Irwell is too polluted to fish; the sun does not break through the surface algae and it dries up most summers.

CHARLIE MITCHELL/FAIRFAX NZ A drain near the L2 river.

The Selwyn River is the largest of Ellesmere's tributaries. It is known for its poor water quality.

In the 1960s it had a trout run of about 40,000. It was down to a couple of hundred at most.

At Boggy Creek, the water hits the green, polluted lake water like a blockade; The river is brown and murky where it drains the lake. Neither have enough flow to flush the lake.

CHARLIE MITCHELL/FAIRFAX NZ A drain near the Irwell River.

Tests have showed the major tributaries have elevated levels of nitrogen, E.coli and sediment.

Kent said many of the area's rivers and streams were too polluted to fish and anglers must venture into the high country.

"You've got to go down to the Opihi or into the mountains somewhere. Most of the streams in Canterbury have just been thrashed.

SUPPLIED Harts Creek in the early 2000s was heavily polluted.

"It's been a tragedy. All those streams and rivers that flow into Ellesmere, apart from Harts Creek, have been destroyed."

Harts Creek was badly degraded by the late 1990s, but was restored in a collaborative effort between farmers and local authorities.

It is the exception, not the rule. Water quality in most of the tributaries remains degraded, but there are signs of improvement.

WAIHORA ELLESMERE TRUST Harts Creek after its restoration.

"Recently we have seen improvements in the phosphorus, sediment and E.coli concentrations in these streams as a result of stock exclusion and better riparian management," Environment Canterbury (ECan) chief scientist Dr Tim Davie said.

"These streams have suffered from both low flows and poor water quality."

Nitrogen levels were a longer-term issue, because of the lag effect in the groundwater. He said low rainfall was the main driver of recent low flows, although extraction for irrigation contributed.

Cleaning up the waterways would be crucial for cleaning up the lake.

"The water quality of these rivers has a large effect on the lake as they deliver most of the nutrients into it," Davie said.

"The poor health of these lowland streams was a major factor in setting up the Canterbury Water Management Strategy and it is a key target of the Strategy to improve the health of these streams."