Liz Favot remembers when she first saw the waters outside her cottage on Lake Nipissing, Ont., turn a murky green. It was in the summer of 2020. “This cottage is my whole heart,” she says. “The first time I saw cyanobacteria at the beach that I grew up swimming at was just crazy.”
Water near the shoreline was the colour of pea soup, and Favot, an aquatic ecologist and an assistant professor at Laurentian University in Sudbury, knew she was probably looking at potentially toxic cyanobacteria, also called blue-green algae. Not all green water is from harmful algae, and not all cyanobacteria look like someone spilled all the Chartreuse. But for the next few days, her family brushed their teeth and washed dishes with bottled water. Swimming at the beach was a no-go, and now when there are blooms, Favot is careful not to let her Norfolk terrier, Rory, drink or even wade in the water. Just in case.
Favot’s grandfather built the cottage in the 1950s, and when she was growing up, she never saw cyanobacterial blooms. “Now, there’s usually a couple of weekends a year where this happens,” says Favot.
A higher incidence of harmful algal blooms is one of the most visible effects a warming climate has on lakes. In addition to more algae, climate change will bring shorter winters, extreme weather, and waters affected by the less obvious processes of browning and stratification. And each of those will have ripple effects for the communities near water.
“Virtually every environmental problem in lakes is worse with warming,” says John Smol, a lake biologist at Queen’s University. Although shorter winters and longer summers might sound appealing—promising more recreational time at the cottage—they can have complex impacts on lake ecology. A 2020 paper published in Nature Reviews estimates that in the last 150 years, ice duration has declined by an average of 28 days in the northern hemisphere. One direct impact of that is a shorter window for ice fishing. “There are some places where ice fishing is a major economic component of the town’s finances,” says Smol.
Early ice-out dates also have important implications for stratification, the formation of different thermal layers in the lake. The process starts in the spring, when most of the water is cold (4°C) and dense, and dissolved oxygen is distributed throughout the lake. As temperatures heat up for summer, warmer, lighter water floats to the surface, while colder, denser water sinks to the bottom, creating stratified layers that resist mixing up and down. That’s why when swimming in a lake, your toes can suddenly graze an icy current while the rest of you stays warm. At the surface, oxygen from the air dissolves into the lake, but because the lake is divided in layers and not mixing, oxygen isn’t reaching the bottom. Shorter winters and longer summers mean that the lakes are stratified for longer. “The longer you’re stratified, the less oxygen is going into deep water,” says Smol. That has myriad effects.
For one, many fish species, such as walleye and trout, prefer cool or cold water and have high demands for oxygen. More stratified waters mean that there’s less oxygen for these fish, and their populations will likely establish themselves in colder water bodies. As conditions become less habitable for trout and walleye, warm-water species like bass and sunfish are displacing them.
Second, stratification creates conditions more favourable for harmful algal blooms. Blue-green algae already prefer the balmier weather and calmer near-surface winds that can be brought on by climate change. “We’ve made a perfect storm for these types of algae,” says Smol.
Favot is already witnessing these effects from her Lake Nipissing cottage. “Lake Nipissing is massive,” she says, but despite being the third largest inland lake in Ontario, the average depth is only around four metres. Being wide and shallow means the lake is usually well mixed, but a 2024 study by Favot showed that more parts of the lake are stratifying now, with low oxygen conditions fuelling cyanobacterial blooms. Her research, which analyzed sediment cores from the bottom of the lake dating back 250 years, confirmed that algae production has reached its highest levels in the period studied. While algal growth is normal in a lake, changing climate conditions favour the runaway proliferation of some toxic species.
Across the lake from Favot’s cottage, residents of Callander Bay report putrid smells, and the municipality is plagued with annual blooms. Cyanobacterial blooms don’t just impact swimming, boating, and other recreational activities. They can be deadly for pets, and they can even reduce the resale value of your cottage. A 2022 study predicted that property prices on Lake Erie will decrease by around 1.7 per cent for every microgram of algae toxin in the water. Another study looking at lake properties across the United States found that a 10 per cent increase in cyanobacteria in the water correlated with a 3.5 to 4.3 per cent reduction in home value.
“In the 1970s, people thought algal blooms were caused by higher concentrations of nutrients,” says Smol. And they weren’t entirely wrong. Fertilizers from fields and farms contain high concentrations of nitrogen and phosphorus, which get washed into rivers and lakes. Just as the nutrients fertilize plants, they also spur algae growth. “That was a great white whale that was hunted,” says Smol, as environmental regulations and improved management curbed nutrient runoff. “The problem is that now we’re seeing these algal blooms at lower and lower nutrient levels.”
Favot says that nutrient runoff in Lake Nipissing was the highest in the 1970s, yet algal blooms have proliferated in the last 20 years. She recalls her doctoral research on Dickson Lake in Algonquin Provincial Park in 2016, after an algal bloom first appeared in 2014. “Normally, it’s very clear, but the entire lake was like pea soup, from algae,” she says. It wasn’t clear why—the lake is pristine and remote, only reachable by lengthy portage, and was closed to overnight campers. As a result, it’s untouched by nutrient runoff, so the unprecedented bloom startled scientists.
What triggered the bloom, Favot theorizes, was another ripple effect of climate change. “The ice-out date that spring was actually surprisingly late,” she explains, and it was followed by a rapid swing to unseasonably warm weather. Favot hypothesized that because the spring mixing period was so short, the bottom depths of the lake were never well oxygenated. As the lake stratified, extralow oxygen levels caused an ecological chain reaction called nutrient loading, in which low oxygen conditions release phosphorus from the bottom of the lake. This dissolved phosphorus then fuelled cyanobacterial growth. (A toxic algal bloom hasn’t struck Dickson Lake since.)
Just as climate change is providing the perfect conditions for algae in lakes, balmy temperatures are also ideal for brewing storms. Warmer air holds more moisture, warping the hydrological cycle and leading to more dramatic weather events. In cottage country, that usually means periods of drought and flooding. In May this year, snowmelt, heavy runoff, and rising water levels in the Nipissing-Sudbury area prompted lakeside residents to leave urgently, with many homes suffering structural damage.
At her cottage on Nipissing for the Victoria Day weekend, Favot spent a couple hours dressed in enormous hip waders, inspecting a boathouse door that was damaged during a flood. The water level was around a foot above the floorboards. People lose their docks and gear stored near the water all the time, Favot says, and because the docks were underwater, people couldn’t access their boats.
Some climate models predict that by the end of the century, an extreme rainfall event that currently occurs once every 20 years in Canada could happen every five years. And torrential rains can have dramatic impacts on lake ecology, as leaf litter, soil, and other detritus washes down from the shore. “In 48 hours of a storm, you can get more nutrients flowing in than typically come in a month,” says Smol. This sudden nutrient runoff can trigger algal blooms, as well as contribute to a phenomenon known as browning.
Smol compares the browning process to making tea: just as soaking tea leaves in water turns the liquid brown, dissolved organic carbon from vegetation, leaf litter, and conifer needles can darken the water. His research shows that lakes are increasingly becoming browner. In part, it’s a consequence of less acid rain, he explains: acid can precipitate dissolved organic carbon out of the water. But climate warming may have pushed lake browning beyond the levels we once saw in the 1800s. Smol thinks that’s because warming has brought on more vegetal growth in general, which can lead to more browning. “Its like there’s more tea leaves going into the water,” he explains.
Browner water can block out sunlight for aquatic plants and algae, which has down-the-line impacts on lake ecology. A 2016 study looking at the effects of brownification on plankton and perch found that dissolved carbon reduces the amount of omega-3 fatty acids produced by plankton. In turn, levels of those healthy fats (the ones you may be buying supplements to get) are lower in the fish at the top of the food chain. The fish are less nutritious. And if the waters are dark enough, predatory fish that rely on eyesight could have a harder time hunting. Dissolved carbon can even give water an earthy or metallic flavour; removing it can complicate water treatment.
And some of Favot’s research suggests that browning also favours—yet again—cyanobacterial growth. A darker colour means the water can heat up more. It’s just one more factor bolstering conditions for growth. “We didn’t realize how bad the situation would get with all these new stressors,” says Smol. “Lakes are being subjected to a thousand cuts.”
While lake science is evolving and we’re seeing some unexpected effects attributable to climate change, Favot says the advice cottagers have heard before still applies: limit nutrient runoff to lower the likelihood of triggering blooms, make sure septic systems are working properly, and forgo fertilizer anywhere near the lake. Meanwhile, scientists will keep trying to untangle the complex ecosystem dynamics to understand what keeps our lakes healthy. After all, scientists are cottagers too.
Science and travel writer Marina Wang is based in Victoria, B.C. Her work has appeared in Canadian Geographic, Hakai Magazine, and The Atlantic.
This story originally appeared in our Summer ’26 issue.
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