But new research says the green slime is not an invasive species wreaking havoc across Canada and around the world, as once believed.
The study by Environment Canada and Dartmouth College in New Hampshire found the unsightly slime is caused by a native species of algae, Didymosphenia geminata, responding to changing environmental conditions.
"I guess this is in the eyes of the beholder but it doesn't look very good. It's gotten the name 'rock snot' and when there are long filaments of it, it can look like toilet paper," said Brad Taylor, an ecologist at Dartmouth.
"Those are just esthetic problems but those are important ones."
In fact, the offending organisms may have been around for thousands of years but their slimy blooms were rare — until now.
The research found it was the result of low levels of nutrients in the water, said Taylor, who co-authored the paper with Max Bothwell, a research scientist at Environment Canada. That ministry refused a media request to speak to Bothwell about the study.
Taylor said the possible causes include earlier spring melts.
"When you turn on the plants and the soil microbes earlier in the year, then they take up more nutrients so that's less nutrients ... that end up getting washed off into rivers and lakes," he said.
Although the yellow-green algae is not a threat to human health, the blooms can have far-reaching effects, Taylor said.
They change the array of aquatic insects available for salmon and trout to eat. The smaller insects are harder to see and require more energy from the feeding fish.
There is also evidence the blooms increase the abundance of a worm that hosts the parasites that cause "whirling disease" in salmon and trout.
The parasite penetrates the head and spine and eventually causes the fish to swim erratically — or whirl. That leads to difficulty feeding and avoiding predators.
The "didymo" blooms may also result from elevated nitrogen in the environment from fertilizers or the burning of fossil fuels, Taylor said.
Millions of dollars have been spent on eradication efforts but the study published in the most recent issue of the journal BioScience said that money might be better spent.
"It changes the way we approach it," Taylor said.
"If it's a native species then we know that the way to control it isn't by preventing it from getting there because it's already there. It suggests that management and policies should be directed at what are the environmental conditions that are promoting the blooms."