Education authorities said schools will also stay closed Thursday as more thundery weather is forecast.
Flights at Abu Dhabi airport resumed on Wednesday afternoon after being suspended for several hours, and Dubai International also experienced delays, aviation authorities said.
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Images posted on social media showed vehicles half-submerged in flooded streets in Abu Dhabi.
Abu Dhabi's stock market said it suspended trading and cancelled all morning deals after many traders could not reach the bourse.
In Dubai, police registered more than 250 road accidents by midday, local media reported.
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The weather agency in the UAE, which ranks among the world's 10 driest countries, said more rain is expected on Thursday.
The country's annual rainfall stands at 78 millimetres (three inches), more than 15 times less than the amount for an average year in Britain.
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