Dr. David McKeown sent out the alert early Tuesday morning, with temperatures set to hover in the low 30s for the rest of the week.
"The heat and humidity is certainly back for the City of Toronto," said CBC meteorologist Johanna Wagstaffe. "We're under [an Environment Canada] special weather statement for high heat and humidity that will last right through to Saturday. So this is another long, hot spell that we're under."
"For Toronto it's the humidex and smog that will sort of add to the oppressive nature of this weather, right through to Saturday," she said.
The alert issued by the city cautions people to take it easy in the heat, especially those with breathing problems.
It also advises people to check on anyone who might be vulnerable during the heat.
"With the humidity we'll be feeling close to 40 C throughout the afternoon. We're looking at thunderstorms in this hot and humid air, both today and tomorrow," said Wagstaffe.