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More than a foot of rain deluged parts of Houston on Monday, leaving five dead as surging waters flooded homes and highways for thousands of residents who were warned to stay inside.

Gov. Greg Abbott declared a state of disaster in nine counties, hundreds of flights were canceled, mass transit was shut down and schools were closed after a season's worth of rain fell in just a matter of hours. Almost 17 inches of rain had inundated the city by 2 p.m. ET.

This is largest flood event since trop Storm Allison not because of flood levels, because of widespread nature. 9 counties affected #hounews — City of Houston (@houstontxdotgov) April 18, 2016

Bush Intercontinental Airport grappled with nearly 650 flight cancellations and more than 1,100 delays. METRO Houston also suspended all rail and bus services, as swaths of the city and nearby Waller County were walloped with 16.8 inches of rain before noon, according to the National Weather Service.

Jeff Lindner, a meteorologist with the Harris County Flood Control District, warned of a "life-threatening situation" due to flash flooding developing in northwest Harris County. "Stay where you are," Lindner added.

Harris County's chief administrator, judge Ed Emmett, signed an emergency declaration for the county, saying more than 1,000 homes had already been flooded, and city and county authorities had responded to more than 1,500 flooding emergencies.

Houston Mayor Sylvester Turner closed all city buildings and canceled the State of the City address that had been scheduled for Monday. "This is a dangerous situation and I do not want our employees trying to get to work," Turner said. “Do not go out until conditions improve." Houston Independent School District was also closed Monday, according to the district.

Eight buildings were damaged by the water, Turner said, and 43,000 people in the Houston area were without power — down from a peak of 123,000, according to CenerPoint Energy. Turner warned that the situation could get much worse as seven bayous across Harris County had exceeded their banks, and two dams were at risk of breaking.

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“This is an unprecedented amount of rain,” Turner said. “It’s been stubborn, and it’s not moving anytime fast.”

Darius Simon, left, and his son Isaac Hernandez wade through floodwaters as they try to reach Simon's mother to rescue her from her flooded apartment on Monday in Houston. David J. Phillip / AP

Five people were found dead inside submerged vehicles, including two in a car that drove around a barricade and into a flooded underpass, Emmett said during an afternoon news conference. A third person who was driving an 18-wheeler was also found dead, and a fourth person was discovered "in a vehicle with water," city officials said in a statement, adding that it was unclear if the fatality was "directly" linked to the flooding.

In nearby Waller County, Judge Trey Duhon said that a 56-year-old man was found dead inside what appeared to be a car filled with water.

To everyone in Houston, please stay safe and avoid traveling. Our prayers are with you. #HoustonFlood -H — Hillary Clinton (@HillaryClinton) April 18, 2016

Turner said that even though the rain was tapering off — though additional wet weather was expected Monday night — flood levels would remain high. In three areas areas around the city that faced severe flooding and where people remained stranded, workers were conducting rescue operations on Monday afternoon.

In one neighborhood, Greenspoint, where 1,000 people were evacuated Monday morning and transported to a mall, the city’s emergency operations center said in a statement later that it was still mounting “a large-scale effort” — including nine high-water vehicles — to assist people there who remained.

One Greenspoint resident, Diamond Trueblood, told NBC affiliate KPRC that she woke up overnight to the “loud sound of water coming through my walls.”

“My stuff was literally floating,” she said.

She described a failed effort earlier Monday to try and rescue a man who had become trapped in a sinking truck that was floating down the street.

“People were trying to bust out the window with their shoes,” she told the station. “The water, the current. There was no way we could get him. He stayed in the truck. He died.”

City officials were still advising people to stay in their homes on Monday afternoon, saying that "straying into deep or fast moving flood waters means certain death." In video footage in Greenspoint, people could be seen standing outside their homes beside flooded roads.

"They're completely stranded," Trueblood told KPRC. "No food. No water."

During a news conference, Turner was asked about lengthy rescue times and increasingly loud complaints from residents. "We are responding, and we’ll continue to respond until every single person is in a safe and dry area," he said, later adding that "for anyone to suggest that a community has not been attended to…would be a serious misstatement."

PHOTOS: Houston Paralyzed By Heavy Rains, Flash Floods

North of Houston, in Magnolia County, assistant Fire Chief Kevin Walters told NBC News that 50 high-water rescues had been conducted since 10 p.m. Sunday. At an equestrian center north of the airport, dozens of horses were trapped in floodwaters — and video footage captured their dramatic rescue.

Weve heard that most of the 80 horses at Cypress Trails have been rescued. A few still loose but not grave danger. Will update when we hear. — Official Ed Emmett (@EdEmmett) April 18, 2016

In Houston's Museum District, just south of downtown, at least five cars could be seen submerged on a low-lying highway, 36-year-old Dakota Smith told NBC News, while on a street northwest of downtown, a local television reporter conducted his own high-water rescue just before going live.

In a KTRK video, reporter Steve Campion can be heard on-camera repeatedly saying "why are you doing that?" as a black Honda drives toward a flooded underpass; moments later, the vehicle is floating, then sinking, and Campion is shouting, "Dude, you got to get out of the car."

VIDEO: Reporter Steve Campion rescues driver trapped in high water in Houston on live TV https://t.co/El0gMQcPlu pic.twitter.com/6S9g0F2yOB — Eyewitness News (@ABC7NY) April 18, 2016

After a confused-seeming elderly man emerges from the passenger-side door, Campion tells him to swim, then rushes toward the man as he struggles through the water.

"I didn't think the water was that deep," the man said he stepped onto higher ground.