Parts of the city were pounded by large hail stones and roads were flooded with muddy rainwater. The downpour left some cars and buses submerged or stranded.
Footage from broadcaster Haberturk showed a city bus half submerged near a bridge in the city's Unkapani district. Some of the passengers left the bus and waded through the flooded road while others climbed on top of the bus's roof.
Other footage showed waves of hail and rain cascading down the stairs of the Taksim metro station.
Two people were injured when the wall of an old cemetery collapsed near a busy street, the Daily Sabah said.
A large crane toppled at Haydarpasa port, near the southern entrance to the Bosphorus, causing an explosion and a fire that was later brought under control, it said.
It was the second time this month that heavy rains flooded streets and disrupted transport in Istanbul.
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