A "lethal cocktail" has decimated the fish population living in and around the Lake District's "jewel in the crown" - according to fishermen and scientists.
Young salmon and trout with damaged gills have been found by the Environment Agency in the River Leven, which has Windermere as its source.
In the past, the Leven was a prime spot for salmon and trout anglers who came from across the country to enjoy their sport.
"I started fishing in the Lake District in 1990 and I very soon realised that all was not well, indeed what I saw was and still is a national tragedy," said Patrick Arnold, who has been teaching people to fish in the area for 15 years.
Temperature change and pollution were all elements in a "lethal cocktail," he said, which had caused the salmon and trout population in the Leven and Windermere to plummet.
"Windermere has changed dramatically over the last ten years, with a knock on effect to the River Leven. There has been a steady decline in catches by fly fishermen of brown trout. To say that catches have now collapsed would not be an over statement," said Mr Arnold.
However, although Mr Arnold reports plummeting numbers of trout, he says the size of the remaining fish has dramatically increased; and the number of perch in the lake has also exploded.
"This shows that there has been a change in the eco system and that the stocks are not healthy. The Leven has been decimated," he said.
The Environment Agency is also concerned about the falling numbers of trout and salmon in both the river and the lake. There are fears that fish found with damaged gills could indicate that changes in the water's oxygen supply has put a strain on their bodies.
Jeremy Westgarth, of the EA, explained that the "historical legacy of the last 20 to 30 years" including environmental and farming changes meant that more algae blooms were growing in the water. These were encouraged by the nutrients found in water pollution, he said, as well as by mild temperatures. The increase in algae causes oxygen levels in the water to change, especially affecting the salmon and trout populations.
Thanks to the efforts of anglers and conservation groups concerned about the future of the area, populations of salmon and trout are beginning to stabilise.
However, Dr Roger Sweeting of the Freshwater Biological Association, based at Ambleside, warned that it may be too late to reverse past damage.
"You have only to speak to old people who used to fish in Windermere to see that we are on a pretty precipitous slope and I don't know if we have done too much damage already," he said.
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