While roads across the region flooded, a stretch between Amherstburg to the east of Harrow got the most rain by early Thursday morning.
Environment Canada said as of 8 a.m., Amherstburg had 184.8 mm of rain since midnight.
The agency has ended its severe thunderstorm watch, but a rainfall warning continues, and it warns the rain isn't done with the region yet. Another 75 mm could fall Thursday night when new thunderstorms enter the area.
Essex Mayor Sherry Bondy said the cleanup will be immense.
"There is large-scale flooding, and almost every road has been impacted," she said. "Unfortunately, we are getting sanitary backups in people's homes."
Bondy said the sewer system in her town is overloaded.
"If you do not need to shower, do laundry, flush the toilet, please do everything you can do possible to reduce the amount of strain on systems," she advised. "Crews are out to make sure all of our pumping stations are working."
The Mayor of Kingsville, Dennis Rogers, made the same appeal, calling on residents to conserve water.
Related story: Boil water advisory issued for Kingsville
He also warned residents with severe flooding in their basements to stay out. Once water levels rise above electrical outlets, entering the water can be extremely dangerous.
Amherstburg Mayor Michael Prue planned to visit areas in his municipality that suffered flooding and tree damage on Thursday. He told WindsorNewsToday.ca that damage in Amherst Point and McGregor was especially severe.
He has also asked his director of public works to report back to councillors on how the town can better prepare for extreme weather in the future.
Prue said Amherstburg does not have backup generators at its pumping stations, and the report would explore the feasibility of installing those.
"I don't know the costs or how big they would be, but I've asked him to put something together so council can understand that," he said.
The deluge slowed the morning commute as traffic lights flashed red and roadways became waterways across Windsor and Essex County.
Ditches overflowed, and fields turned into lakes. A portion of County Road 50 near Star Beach washed away, and officials warned drivers to avoid Erie Street North, Arthur Street and Sunset Drive in Harrow.
The Essex Region Conservation Authority has issued a flood warning for the Town of Essex, Kingsville, Leamington, Lakeshore and Pelee Island. A flood watch is still in effect for the rest of the region. Both notices will be in effect until noon on Friday.
The authority is monitoring flooding on many roadways throughout the region. Director of Watershed Management Services James Bryant cautioned driving on those roads is risky.
"There are areas that I've seen where the pavement is starting to shift a little bit, and while the water may not be deep, it's fast moving. You can run into some issues there with your vehicle," warned Bryant.
There is flooding on County Road 50 between County Road 41 and County Road 13. Significant water covers those streets heading south towards Lake Erie.
In the Town of Kingsville, reports include water over the road on County Road 20 between Graham Sideroad and County Road 45 (Union Avenue).
In the Municipality of Lakeshore, reports include flooding on St. Clair Road and flooding on Lakeshore Road 241 due to the overtopping of the Ruscom River.
Flooding also caused multiple crashes on the E.C. Row Expressway on Thursday morning.
Hydro One reported scattered power outages across Essex County. Crews resolved most by 9 a.m.
E.L.K.Energy restored power in Kingsville by 9 a.m., but there was no indication when it would come back on in Harrow.
In Windsor, the lights went out in South Windsor on Wednesday evening, and Enwin Utilities restored power by 3 a.m. on Thursday.
Environment Canada reported 88 mm of rain for Windsor. The city said it had only eight calls to 311 about basement flooding, 22 reporting road flooding or blocked catch basins, and 23 reports about tree damage.
With files from Maureen Revait.