Troubled Waters: Why Ontario's Lakes Are in Crisis — and What's Being Done About It

If phosphorus is Ontario's legacy pollution problem, PFAS — the class of synthetic "forever chemicals" used in everything from firefighting foam to nonstick cookware — is its emerging one, and it's arguably harder to solve.

The starkest example is North Bay, where firefighting foam used for decades at the Jack Garland Airport and the adjacent 22 Wing Canadian Forces Base contaminated soil, bedrock, groundwater, and nearby waterways — including Trout Lake, the city's primary drinking water source. Engineering firm Stantec's assessment found contamination extending into Lake Nipissing and several connecting creeks. CBC reported in February 2026 that Trout Lake's PFAS levels sat around 58 nanograms per litre — below Ontario's advisory guideline of 70 ng/L, but well above the stricter 30-ng/L objective Health Canada published in 2024.

The contamination's history has become part of the story itself. Reporting by the Investigative Journalism Bureau found that the Department of National Defence had identified elevated PFAS levels around the base as early as 2012, but didn't tell the City of North Bay until 2016 and didn't disclose it publicly until 2017. In late 2025, North Bay residents filed a proposed class-action lawsuit against the city and the federal government, seeking remediation, safe drinking water, and $105 million in damages for people living within three kilometres of the base. Separately, the city and federal government are pursuing a $122-million cleanup.

North Bay isn't unique — it's just the most visible case in a pollutant that's turning up across the Great Lakes basin. Federal scientists testing Hamilton Harbour on Lake Ontario have measured PFAS concentrations as high as 25 ng/L, and other testing near a wastewater treatment plant discharge point found levels roughly triple that. Because Lake Ontario sits downstream of every other Great Lake and is the most urbanized and industrialized of the five, researchers with Environment and Climate Change Canada have found it carries the highest PFAS concentrations of the group. Ontario has issued fish consumption advisories related to forever chemicals in Lake Superior, Huron, Erie, and Ontario, as well as the St. Lawrence River.

Part of what makes PFAS so difficult is that Ontario's wastewater infrastructure was never built to catch it. Much of the province's treatment system dates to the 1960s and '70s, designed to strip out phosphorus and ammonia — not the thousands of pharmaceuticals, microplastics, and industrial chemicals now flowing into it. Researchers at Toronto Metropolitan University have been documenting the scale of the gap and pushing for Canada to adopt a coordinated regulatory approach to these "contaminants of emerging concern," something that currently doesn't exist in Canadian law the way it increasingly does in parts of the United States.

There's also a whack-a-mole dynamic at play: as regulators phase out older, well-studied PFAS compounds like PFOA and PFOS, industry has shifted to newer, shorter-chain replacements that haven't been as thoroughly tested — meaning some of the improvement in long-term monitoring data may mask a shift in the type of contamination rather than its elimination.

All of this — legacy chemicals, forever chemicals, algae, warming water, invasive species — eventually funnels down to the same place: the fish themselves, and the people who catch and eat them. For an angler's-eye view on what's safe on the plate, see our guide on eating the fish you catch in Ontario.

Ontario has issued fish consumption advisories for decades, and the province's Guide to Eating Ontario Fish now covers more than 2,700 fishing locations, with restrictions keyed to mercury, PCBs, dioxins, and — increasingly — PFAS. The good news is real: peer-reviewed analysis of roughly four decades of contaminant data from Lake Ontario found a clear downward trend in both mercury and PCB levels in walleye and lake trout, evidence that decades-old bans on PCBs and reduced industrial discharge have paid off.

The bad news is that the legacy hasn't cleared. That same research found lake trout still exceed the PCB consumption threshold more than 80% of the time across every site studied — a reminder that these chemicals, banned in the late 1970s, still linger in the fatty tissue of long-lived, high-fat fish species half a century later. PFAS complicates the picture further: unlike PCBs, which concentrate in fat, some PFAS compounds distribute evenly through fish flesh — meaning trimming skin and fat, the usual advice for reducing contaminant exposure, doesn't help.

Then there's what the water itself is doing to fish habitat. Lake Erie's central basin develops a seasonal "dead zone" most summers, when decomposing algae blooms consume dissolved oxygen faster than it can be replenished, leaving water too oxygen-poor for most species to survive. In August 2012, tens of thousands of fish — including drum, perch, and smelt — washed up dead along roughly 25 miles of Canadian shoreline between Erieau and Port Stanley. Commercial fishers working nearshore trap nets in the area have described the same pattern repeating in some years: dead or lethargic fish showing up as low-oxygen water moves inshore. Researchers at Ohio State University's Aquatic Ecology Laboratory note that while hypoxia is bad news for cold-water species like lake whitefish, the same nutrient-rich conditions driving algal blooms can actually benefit yellow perch and walleye, at least for now, by feeding the plankton lower in the food web. It's a fragile, shifting balance rather than a straightforward decline.

Invasive species have reshaped Ontario's fisheries just as much as pollution has. Sea lamprey, a parasitic invader, drove serious historical declines in lake trout populations and their associated fisheries across the Great Lakes. More recently, the round goby — a small, aggressive bottom-dweller first found in the Great Lakes in the early 1990s and believed to have arrived in ship ballast water — has out-competed native species for food and habitat and preys heavily on the eggs and young of sport fish. In Lake Erie, goby predation on smallmouth bass nests has been severe enough that Ohio closes its smallmouth bass fishery every May and June, the two months that historically accounted for half the annual catch, so male bass can defend their nests. The goby story isn't purely negative, though: the fish has also become an important new food source for walleye, yellow perch, and lake trout, and some researchers believe it has helped growth rates in Lake Ontario bass populations that now feed heavily on gobies.

For anglers and the businesses that depend on them, the stakes are significant. Recreational fishing across the Great Lakes region generates an estimated $8.3 billion annually, and Ontario's fisheries — supporting walleye, yellow perch, muskellunge, bass, and northern pike fisheries in particular — are a substantial contributor to that figure. There have been genuine bright spots: rehabilitation of habitat and improved water quality along Toronto's waterfront has brought back walleye, bass, and pike to a degree that sport-caught fish there are now considered safe to eat, turning a formerly industrial shoreline into a working urban fishery. But the broader trend lines — a warming, more variable lake environment, new and legacy contaminants moving through the food web, and invasive species still rewriting who eats whom — mean the fishing itself has become one more place where Ontario's water quality problems show up first.