An investigation into the safety of the sludge pools has been launched by Scottish Water, while environmentalists are demanding the sites be cleaned up.
The lagoons are sighted at Wigtown, Barrhead, Coatbridge, Falkirk, Cupar and Inverness, and across Argyll, Aberdeenshire, Sutherland, Orkney and elsewhere.
The Scottish Environment Protection Agency (Sepa) said 18 sites are left over from when drinking water was treated with an aluminium compound to remove impurities. They are now contaminated with the metal, which has been linked to breast cancer and Alzheimer's.
"There is a possible risk of such aluminium leaching," Sepa said, though its "binding nature" meant it was likely to stay in the sludge.
Green MSP Alison Johnstone said: "Many people will be shocked to learn of these potentially toxic lagoons dotted around Scotland. It's vital Scottish Water and Sepa properly assess them and figure out what to do with them."
Dr Richard Dixon, director of WWF Scotland, said: "Aluminium is not something we want leaching out because it represents a danger to human health and to wildlife. This is a large and potentially nasty legacy Scotland needs to deal with."
It is uncertain how much sludge is in the pools, but Sepa said one, at Cupar in Fife, may contain up to 2000 cubic metres.
Sepa manager Colin Anderson said: "Almost all these sites are still within the curtilage of existing Scottish Water works and are being maintained and managed to some extent."
Scottish Water said it had inherited the pools, which date from when councils provided water and waste treatment, when it was formed in 2002.