Sulphur, nitrogen and ammonia spewed out by power stations, factories, vehicles and farms have contaminated waters in Galloway, the Cairngorms, the Trossachs and north-west Scotland.
This has damaged populations of brown trout, Atlantic salmon and other fish, as well amphibians such as frogs and insects. There are also fears for birds and mammals that feed from waterways.
The acid contamination has persisted despite decades of international efforts to cut the pollution that causes it with recent forecasts that there will still be 130 dangerously acidic lochs in 2020.
Dr Richard Dixon, director of WWF Scotland, said: "Our wildlife and wild places are suffering today across large areas of Scotland. People will be very surprised to learn that a problem they thought was fixed in the 1980s is still with us 30 years later."
Although acid emissions have been reduced, concerns about the effects are still very real, he said, adding: "We need to learn this very important lesson about how long it takes to fix major environmental harm even when you've taken it seriously."
The worst problem is in Galloway, where 49 lochs have been found to exceed what scientists call "critical loads" of pollutants. Above these levels, acidity is high enough to damage wildlife and degrade the natural environment.
Among the lochs affected are Clatteringshaws in the Forest of Galloway, Loch Doon in Carrick and its appropriately named neighbour, Loch Muck. Acid pollution levels in Galloway are about twice as high as elsewhere.
There are 44 lochs in the Cairngorms and the Grampians acidified in breach of critical loads, including Loch Morlich, Loch Avon and the Pools of Dee.
A further 32 lochs are contaminated in the Trossachs and central Scotland, including Loch Chon and Loch Drunkie. Another 74 acid-affected lochs are spread across north-west Scotland, with one in the Borders.
Dr Chris Curtis, who led research at University College London (UCL) and now lectures at the University of the Witwatersrand in Johannesburg, said: "Critical loads are still exceeded in some of the most sensitive upland regions of the UK, and many of these occur in Scotland."
The Scottish Government highlighted the impor- tance of international co-operation in cutting pollution.
A spokesman said: "The Scottish Government and its agencies actively monitor acid rain levels and its impact, and through the UK Acid Waters Monitoring Network we work with other UK administrations to scrutinise levels of pollutants in the water environment."