AFPTV footage showed partially submerged cars struggling to drive through standing water in the central region of Qassim, one of the areas hit hardest overnight.
"The rain continued for seven hours from the afternoon until near midnight in very large quantities," said Mohammed, an Egyptian resident of Buraidah, capital of Qassim, who spoke to AFP on the condition that only his first name be used.
"Water accumulated to a height of more than 10 centimetres (four inches) in front of the residence and prevented us from going out to the street. The sound of thunder was loud and lightning was illuminating the city."
The national meteorological centre issued red alerts for Qassim and other areas including eastern province on the Gulf, the capital Riyadh and Medina province bordering the Red Sea.
It warned of "heavy rain with strong wind, lack of horizontal visibility, hail, torrential rains, and thunderbolts".
Schools in Eastern Province and Riyadh also cancelled in-person instruction and moved classes online.
The Medina education department posted on X pictures of maintenance workers repairing electricity and air-conditioning units and removing standing water from schools.
There was some standing water on Riyadh's roads on Wednesday but traffic was not significantly disrupted.
Rainstorms and flooding are not unheard of in Saudi Arabia, especially in winter, and larger, more densely populated cities can struggle with drainage.
Such problems are an annual occurrence in Jeddah, the port city on the Red Sea coast, where residents have long decried poor infrastructure.
Floods killed 123 people in the city in 2009 and 10 more two years later.
This week's heavy rainfall in Saudi Arabia follows the intense rains that lashed the region in mid-April, killing 21 people in Oman and four in the United Arab Emirates, which received the heaviest rainfall since records began 75 years ago.
Global warming caused by fossil fuel emissions "most likely" exacerbated those rains, an expert group of scientists said in a study published last week.
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