Two people in Jeddah were electrocuted by a lamp post when they attempted to cross a flooded street, while an 11-year-old boy drowned in Yanbu further north.
Two children were also missing in the north-western province of Ha’il, while a third child was rescued in a flooded valley there.
Footage and photographs broadcast on Saudi-owned Al Arabiya television showed cars being swept along Jeddah streets and people using boats to navigate districts of the city.
Severe thunderstorms forced schools and universities to suspend classes in the western city, along with nearby Mecca. The civil defence said schools would remain closed on Wednesday.
Meanwhile, Jeddah’s King Abdulaziz International Airport said eight domestic flights had been delayed due to heavy rain, while one international flight was diverted to Medina.
“Air traffic is now back to normal,” the airport said on Tuesday afternoon.
Heavy rain struck other parts of Saudi Arabia, including Medina, Hail and Arar.
“The next few hours will see more moderate rains in Jeddah and its northern areas,” said Hussein Al Qahtani, a weather department spokesman.
Even heavier rains fell in the north-western city of Tabuk, near Jordan, where 46 millimetres were recorded since Monday, Mr Al Qahtani said.
Following cool winds, moderate to heavy rains would on Wednesday move east to the Riyadh region and other areas, he told Al Ekhbaria television news channel.
Floods killed 123 people in Jeddah in 2009, and about 10 people two years later.
The National Center for Meteorology and Seismology in the UAE says rain is expected in the country on Friday.
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