I went fishing the other day in – don't gag, now – Toronto Harbour. I didn't catch anything, but then I'm a crummy fisherman. It wasn't for lack of fish. There are plenty out there, and not just the carp and suckers I used to see floating belly-up when I sailed there as a kid in the 1960s. No, these are proper sport fish.

My conservation-authority guide showed me the best spots. You can catch bass in the still water of the Toronto Island lagoons and walleye in the Outer Harbour. In the slip at the foot of Spadina, you can even catch northern pike, a chisel-faced, sharp-toothed predator that sometimes gobbles passing ducklings.

The return of big fish to the Toronto waterfront is part of a bigger, often overlooked story: the rebound of the city's natural environment. The city's air and water are the cleanest they have been in decades.

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Ontario's Ministry of the Environment says testing shows falling levels of bacteria and phosphorous in Toronto waters and of lead and mercury in the sediment of Humber Bay and the Inner Harbour. Contaminants such as dioxins, furans and PCBs are down by as much as 90 per cent over the past 40 years. As a result, most sport fish are as safe to eat as those you might catch in cottage country.

"Contrary to popular belief," says the 2012 City of Toronto guide Fishes of Toronto, "the quality of water in Toronto's watercourses and Lake Ontario is generally quite good."

Toronto waters are not only safely fishable, but swimmable, too. Eight of the city's 11 beaches now qualify for Blue Flag status, an international measure of cleanliness. At Centre Island beach, the number of days when bacteria exceeded recommended swimming levels fell to just three last summer, from 62 in the 1995 season.

As for the air, levels of almost all major pollutants are down sharply over the past decade as the result of tougher pollution monitoring, upgrades in automobile- emission controls and the phasing out of coal-fired power generation. Measurements at Toronto's four air-testing stations show that nitrogen dioxide has decreased 36 per cent, carbon monoxide 74 per cent, sulphur dioxide 65 per cent and fine particulate matter 24 per cent.

These encouraging facts clash with how many of us view cities. To swim, fish or even breathe freely, people think they have to flee to the countryside. The postwar exodus to the suburbs was driven in part by the perception that cities were foul, overcrowded, unhealthy places best abandoned for greener pastures.

That view lingers on despite the huge improvements in the urban environment. Better sewage treatment has cut water-pollution levels and controls on phosphorous from detergents, and farm run-off has reduced the algae blooms that were fouling the lake. Yet, "if you stop people on the Gardiner Expressway and ask: 'What do you think of Lake Ontario? Is it polluted?' most people would tell you yes," says Gord MacPherson, who works for Toronto Region Conservation on restoring fish habitat. "In reality, it's not. The perception is based in the seventies and we still can't get it out of our heads."

He calls the recovery of the Great Lakes "one of the biggest ecological success stories in North America, if not the planet."

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In a tour of the harbour with other fisheries experts, he pointed out thriving man-made wetlands on Toronto Island where herons waded and red-winged blackbirds chucked among the rushes and cottonwoods. Back at the pier, he showed off big pike, bass and bowfin, just pulled from the Outer Harbour. A fisheries crew was fitting them with electronic tags to trace their movements.

Fish surveys show that panfish, yellow perch, largemouth bass and smallmouth bass are increasing, while the white sucker, which is tolerant of poor water quality, is on the decline as the water gets cleaner and other species move in. Smaller fish like the emerald shiner are also on the rise, providing good eating for the bigger species. Still further down the food chain, studies show a comeback of the so-called "benthic community" of bottom-dwelling worms, bugs and other organisms that fish feed on.

Toronto's environmental comeback still has a long way to go. Storms like the big one last month still flush sewage from old-fashioned combined sewers into the lake. Road salt and motor oil still flow from the drains into the rivers and creeks. Levels of ground-level ozone, a component of smog that forms when volatile organic compounds and nitrogen oxides react in sunlight, are actually up five per cent in the last decade. Scientists are concerned about a puzzling resurgence of phosphorous in parts of the Great Lakes.

But the city has come a long way since the days a century back when, according to the City of Toronto's website, "water in Toronto Bay was a cesspool of city runoff, industrial pollution and human waste." Despite everything you hear about the fouling of the global environment, in our little corner of the globe, at least, things are getting decidedly better.

I bought a casting rod and big shiny lure for this article. I'm going back to the waterfront for one of those pike.