It was one ecological disaster we thought we'd largely licked.

But in an "insidious" echo of the 1980s acid rain crisis, lakes in parts of North America and Europe are now experiencing severe calcium depletions that scientists are terming an "osteoporosis" of the water, a new study in the journal Science suggests.

The paper's Canadian-led research team says acid rain – a lake-killing cause célèbre largely tamed in the past two decades – expelled much of the calcium from giant tracts of soil during its toxic heyday.

And that calcium loss is now being felt in many of the lakes those soils feed – endangering entire aquatic food chains as well as the waterfowl that marine life supports.

If calcium levels continue to fall, the potential for many lakes to simply die is very real, says John Smol, a professor at Queen's University and a key study author.

The cycle began when acid components were expelled into the atmosphere by massive industrial plumes late into the 20th century. These emissions have been greatly reduced by government-mandated scrubber technology.

"We've made very good progress on acid rain ... and we have been seeing acidity recovery in lakes," says Smol. "But we didn't quite realize at the time that acid rain had a whole bunch of other possible side effects."

Abetted by logging operations, which also deplete calcium levels in soil, acid rain pushed much of the mineral out of the ground in many parts of this continent over many decades, Smol says. This was especially true in areas of the Canadian Shield where the dirt is not deep.

And while the process initially caused calcium levels to soar in many lakes – as the displaced mineral was washed into the streams and rivers that feed them – those levels eventually dissipated. And there was no more soil-based calcium to replace it.

"Since the Ice Age, for 12,000 years calcium has been slowly being released from the soils, going into lakes and being used by the lakes," says Smol. "With acid rain we speeded that up really fast and now there's very little left. ... It's what we call aquatic osteoporosis."

The main culprits in acid rain, sulphuric and nitric acids, are like calcium and carry a positive charge. And as they fall into the ground, their positive charges repel the similarly charged calcium.

Calcium, which helps build bones in humans, is required by all species. But in marine ecosystems, it's especially required by some of the tiny "keystone" species at the bottom of a food chain. And the study, which also included York University researchers, found a creature known as the Daphnia, or water flea, has been especially hard hit.

"It's an integral part of most lake systems. It feeds on the algae and any small fish feed on the Daphnia," says Smol, Canada Research Chair in Environmental Change.

The calcium declines could also prove especially harmful to molluscs and crayfish, whose outer shells require high calcium intakes.

But using the invertebrate Daphnia as an indicator, Smol's team sifted through sediments in three lakes: Plastic Lake near Dorset, Ont. in the Muskoka region, Little Wiles Lake in Nova Scotia, and Big Moose Lake in New York state.

And in all three they found both low calcium levels and a sharp decline in water flea populations, often dating back to the 1970s.

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"A large number of lakes could be similarly effected," says Smol. "It's also probably hitting lakes in Scandinavia, we know in Norway calcium levels are very low. It's probably much more widespread."

University of Waterloo freshwater ecologist Roland Hall says the study introduces a major new environmental concern and should lead to intensive research into the full effects of calcium depletion. "It's a little (like) when we discovered the ozone hole. Nobody was thinking about it, and then you find this hole and everybody is out there trying to figure out what (it's doing)."