It got so badly choked with slimy algae one weekend in June, 1992, that the event became known as Scum Saturday, causing a major alert and leading to questions in parliament.
Now, however, the loch's water quality is the best it has been in more than 20 years, according to a report commissioned by Scottish Natural Heritage.
Both fish and bird-life have benefited from the greatly improved clarity of the water and the diversity and abundance of aquatic plant life.
Scotland's largest lowland loch is nationally important for its waterfowl and has the UK's largest population of inland breeding ducks, as well as thousands of migratory birds.
SNH reports that pochard diving ducks, which eat aquatic plants and are in decline Scotland-wide, have increased in number on Loch Leven – from 1000 wintering birds in 1990 to 2400 in 2007. The increase is thought to be down to the proliferation of underwater plants.
Loch Leven trout fishery, which went into decline in the 1990s due to the pollution, is also improving. Last September, Michael Mackenzie of East Whitburn landed the largest brown trout to be caught in Loch Leven in a century, weighing 9lb 6oz.
Jamie Montgomery, of Kinross Estate Company, whose family owns the loch, said the fishery was "effectively dying" in 1990, with boats sold off. Since then, however, the clean-up has been "remarkably successful". He said: "If you talk to anglers here they'll say it's better conditions than they've had for ages."
Dr Linda May, deputy director of the water programme at the NERC Centre for Ecology and Hydrology, in Edinburgh, which compiled the report for SNH, has monitored the water quality at the loch for 36 years.
She said: "In 1976, we had lots of nasty blooms and the water wasn't very clean, but it's absolutely beautiful now.
"The long-term monitoring programme has given us a good understanding of the links between pollution, climate change and ecological response and this has ultimately led to better water quality. We need to make sure we continue to control the amount of phosphorous going in. It hasn't met the EU water quality target yet, though it's on its way towards it."
In the 1980s, phosphorous pollution from industry, agriculture and sewage was entering the loch in large quantities. As a plant nutrient, it caused blue-green algae to bloom on the surface of the water, blocking light to underwater plants, and water clarity was reduced to a depth of one metre.
It deterred visitors, as algal toxins can cause stomach upsets, eye infections and rashes. In June 1992, during calm weather, a large area of the loch's surface was covered with blue-green algae. The situation was exacerbated when it started to rot, becoming yellow and smelly.
Scum Saturday and its aftermath caused about £1 million of lost revenue to the community due to a fall in the number of people visiting the area for fishing and watersports.
Since then, efforts have been made to reduce phosphorous levels and the water clarity can now reach 4.7m in spring.
Measures included installing phosphorus scrubbing facilities at the local Scottish Water waste water treatment works, promoting better agricultural practices and strict controls on private waste water treatment systems.
Denise Reed, SNH Tayside & Grampians operations manager, said: "This is terrific news - but we can't be complacent; we have to keep up our efforts to make sure the loch's water remains clean and healthy."
Dr May added Loch Leven now had eight tonnes of phosphorous entering it annually, down from 20 tonnes in the 1990s. Such a loch should have five or six tonnes going in to it from natural weathering of rocks and soil.