Rivers and lakes in northern Europe and North America that have turned brown are returning to a more natural, pre-industrialised state, a study says.
Water changing from blue to brown could be a good sign
A major reduction in acid rain since the 1970s has resulted in more dissolved organic carbon entering the regions' waters, researchers suggest.
Writing in Nature, they say soils are becoming less acidic, resulting in more carbon being washed away by rainfall.
The staining has previously been linked to global warming and land-use change.
"The solubility of organic carbon is pH-dependent, so the more acidic a soil gets, the less soluble a number of these organic compounds are," explained co-author Don Monteith, from University College London, UK.
Acid rain is caused by burning fossil fuels, especially coal. Sulphur and nitrogen emissions from large industrial sites, such as power stations, react with water in the atmosphere to fall to the ground as acid rain.
The problem reached its peak in Europe and North America in the 1970s, damaging forests, lakes and even buildings.
Since then, legislation has curbed the amount of the pollutants being pumped into the air.
As the problem subsided, soils became less acidic and more of the organic carbon content became susceptible to being washed away into rivers and lakes.
"This issue was identified about five years ago, and since then there have been a number of papers trying to explain what is going on," Mr Monteith told BBC News.
"A lot of these ideas would suggest that that there is this global process which is linked, in some way, to global warming.
"What we are demonstrating here is that the main driver is acid rain. It is unlikely that this process is occurring globally - it is going to be confined to these industrialised nations that are cleaning up their emissions."
Although the discolouration is a sign that waters are becoming less acidic, Mr Monteith, said many people would view it as a deterioration in water quality.
"The problem is that people have been living with the impact of acid rain for so long that no-one alive today really has an idea of what the waters were like before acid rain took hold," he said.
"A lot of the drinking water in the UK is drawn from upland catchments, where we do have the browner water.
"The public tend not to like any evidence of discolouration so the water industry has to spend quite a lot of money to treat the water to remove the colour."
However, he added that the increased release of dissolved organic carbon was not without problems.
"One impact is the distribution of sunlight in lakes. In some aquatic ecosystems, plants will not be able to grow as deeply as they did before, because light will be attenuated in the upper levels of the lake."
Another potential issue Mr Monteith pointed up was that some toxins, particularly industrial heavy metals such as mercury, copper and aluminium, bind very tightly with organic molecules.
"At the moment we do not know what the implications are for the cycling and transport of these toxic compounds now that the carbon is becoming more soluble."
He said that the team of researchers who worked on the paper hoped the findings would settle the debate about the cause of the brown water and help move things forward.
"We believe that there should be a lot more work going into the consequences of the potential changes in the [carbon] cycle - we don't have any real idea as to the fate of this (dissolved organic carbon)," he admitted.
"In theory, we should be seeing larger amounts of organic carbon reaching the oceans, but we don't really know what happens when it reaches the water and to what extent the carbon will end up in sediments or be lost to carbon dioxide."