The alert is in effect until midnight Friday.
Air quality remained in the hazardous category for the Chicago area Friday morning.
ABC7 Accuweather Meteorologist Tracy Butler said the worst of the air quality will be in the morning hours and conditions could improve in the afternoon hours.
SEE ALSO: Tracking air quality across the Chicago area
Butler said some rain and storms in the afternoon and evening and it is possible the rain mixes with the smoke to leave behind a sludge.
Butler said the air quality should be better on Saturday, but smoky skies could return on Sunday.
Smoke from Canadian wildfires in downtown Chicago
The air is unhealthy for anyone to breathe.
The smoke and haze blanketing the Chicago area is causing low visibility and could create some delays here at O'Hare Airport.
The unhealthy conditions are not only disrupting travel, but also interrupting many outdoor activities.
The pollution forced several major events in the city to be rescheduled, including a Millennium Park summer music series performance and the Chicago Fire match at Soldier Field.
The Chicago Park District officially closed all beaches and outdoor pools designating only indoor ones stay open. They also moved all-day camps inside.
Health experts said the air is unhealthy for everyone to breathe and are encouraging people to avoid or limit time outdoors until the air quality gets better.
"If you can see it, and you can smell it, you're breathing it in...so recommendations right now: if you don't have to go out, then stay home," Dr. Juanita Mora of the American Lung Association, said.
Doctors also recommend that people stay hydrated, which can help the respiratory system in these smoky conditions.