Sulphur, nitrogen and ammonia spewed out by power stations, factories, vehicles and farms have badly 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, including mayflies. There are also fears for birds and mammals that depend on waterways for food, including dippers, grey wagtails and otters.
The acid contamination has persisted despite decades of international efforts to cut the pollution that causes it. And it doesn't look likely to go away any time soon, with scientists forecasting that there will still be 130 dangerously acidic lochs in 2020.
"Our wildlife and wild places are suffering today across large areas of Scotland," said Dr Richard Dixon, director of green group WWF 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 affects are still very real, he argued, 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 also 44 lochs in the Cairngorms and the Grampians acidified in breach of critical loads, including Loch Morlich, Loch Avon and the Pools of Dee. Lochnagar, a lochan high on the mountain of the same name, near Balmoral on Deeside, is polluted.
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 (see map).
A network of scientists commissioned by the UK and Scottish governments have been monitoring more than 850 lochs in the most sensitive areas of Scotland since the 1980s. Their latest results, covering 2006-08, released on request to the Sunday Herald, show 200 sites still exceed critical loads.
This is better than in 1986-88, when nearly 400 sites were contaminated, or 1996-98, when more than 300 were contaminated. But scientists predict 15% of the monitored sites – 130 – will still breach critical loads in 2020 (see table).
"Critical loads are still exceeded in some of the most sensitive upland regions of the UK, and many of these occur in Scotland," said Dr Chris Curtis, who led research at University College London (UCL) and now lectures at the University of the Witwatersrand in Johannesburg.
Despite dramatic reductions in pollution, recovery will take a long time, he cautioned. "The benefits of reducing acid deposition may be delayed because of the legacy of more than a century of acid deposition, some of which is stored in the soils of upland areas," he said.
"Most waters are still a long way from reaching their pre-industrial chemical conditions. Biological recovery of fish and other aquatic organisms lags even further behind."
Dr Rick Battarbee, a former head of the Environmental Change Research Centre at UCL, added: "Evidence from the long-term monitoring of acidified lakes and streams in Scotland shows that conditions are improving but there is a long way to go before most are restored to full health."
According to Jamie Ribbens, the senior fishery biologist at Galloway Fisheries Trust, more than 240 kilometres of running water in Galloway has been polluted by acid rain. This is "severely limiting" populations of fish, particularly salmon, he said.
"These unnaturally low pH conditions are having a significant economic and biodiversity impact through the loss of fish from key upland spawning and nursery areas," he argued.
The Government's environment advisors, Scottish Natural Heritage (SNH) and the Scottish Environment Protection Agency, both stressed the gains that had been made in tackling acid pollution, but accepted that problems persisted.
"Biological recovery in sensitive rivers and lochs has progressed more slowly, partly because the legacy of past emissions is stored in the soils," said SNH's Dr Iain Sime. "Acid-sensitive species such as trout and some plant species remain at risk in sensitive locations."
Bird group RSPB Scotland pointed out that past studies had suggested birds that depend on water like dippers and grey wagtails could suffer through lack of food.
A spokesman said: "We would like to see those surveys repeated now that we are a quarter-of-a-century down the road, to see whether more efforts are needed to clean up lochs."
The Scottish Government highlighted the importance of international co-operation in cutting pollution. "We are committed to playing our part of this necessary global effort," 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."
WHAT IS ACID RAIN
IT was a Scottish chemist, Robert Angus Smith, who first coined the phrase "acid rain" in 1872. It was an inevitable product of the industrial revolution, with the pollution belching around the world.
Unchecked, the burning of coal and other fossil fuels to produce heat and power releases sulphur dioxides and nitrogen oxides into the air. Cars and lorries also emit nitrogen oxides in exhaust fumes.
When these gases mix with water droplets in the atmosphere, they form weak solutions of sulphuric and nitric acids. These then fall to the earth as acid rain, making lochs, rivers and soils more acidic, and also releasing aluminium.
Mountain environments are particularly vulnerable to the pollution, which can be transported over hundreds of miles. It creates a toxic environment for aquatic wildlife that can harm fish, including salmon and trout, as well as insects, plants and possibly birds and mammals.
Acid rain can also damage buildings, historic monuments and statues, especially those made of limestone and marble. Acids react with the calcium compounds in the stone to form gypsum, which flakes off.
Governments started taking a serious interest in acid rain in the 1970s and 1980s. Scandinavian countries complained that tens of thousands of their lakes were being destroyed by acid pollution from the UK and elsewhere.
As a result, measures were introduced to cut pollution from power stations, which have led to major reductions in emissions. Sulphur emissions in the UK have dropped by 95% since 1970.
Across Europe, sulphur dioxide emissions fell by 82% between 1990 and 2010, with smaller falls in emissions of nitrogen oxides (47%) and ammonia (28%). Studies show that this has enabled some lakes and rivers to recover, but progress has been slow, say scientists.
Professor David Fowler, from the Centre for Ecology and Hydrology's site near Edinburgh, said: "Sites are starting to recover, and you can see the signs of recovery, but it will take a long time for them to completely recover, and a few may never recover."
POLLUTION ACROSS EUROPE
A DOZEN countries across Europe have breached air-pollution safety limits, putting human health and the environment at risk.
The European Environment Agency (EEA) says that Austria, Belgium, Denmark, Finland, France, Germany, Ireland, Luxembourg, Malta, the Netherlands, Spain and Sweden all failed to meet agreed ceilings for nitrogen dioxide emissions. The UK met the limits.
Nitrogen dioxide, which is emitted by vehicles and power stations, can damage the lungs, blood and immune system. It also contributes to acid rain and pollutes lakes and rivers.
The EEA, which is an agency of the European Union based in Copenhagen, says reductions in the pollutant over the last two decades have been lower than originally anticipated. This is partly because road transport has grown more than expected.
In a new report, the EEA urges further reductions in emissions. Much has been learnt about the impact of pollutants in recent years, it says, and European countries are falling behind.
EEA executive director Jacqueline McGlade said: "Member states have even further to catch up on air pollution when the latest science is taken into account."