Authorities announced warnings on social media, with heavy rain expected to continue in and around the region until about 10pm on Wednesday.
The Saudi Centre for Meteorology denied hurricanes were forecast in the area.
“The news circulating about the kingdom being directly affected by hurricanes is incorrect because it overlooks semi-enclosed seas,” it said.
Earlier this week, the Saudi Press Agency reported that the kingdom "overlooks semi-enclosed seas in which tropical cyclones do not form, and their direct impact is unlikely".
On Saturday, a red weather warning for the Makkah region was issued, warning people of torrential rain and hail.
Saudi Arabia recorded temperatures of 50ºC this summer.
The world has been enduring record-high temperatures this year. Scientists at Nasa's Goddard Institute for Space Studies said that July 2023 was hotter than any other month on record since 1880.