Images shared on social media and Turkish television showed huge hailstones battering the streets of Turkey's most populated city and cars submerged in the torrential downpour.
Flights at Istanbul Atatürk International Airport were canceled and metro services were suspended, officials said.
A crane overturned at the Haydarpaşa Port, starting an explosion and a subsequent fire.
The city's tram service between the Bağcılar suburb to Kabataş on the banks of the Bosporus was also suspended.
An old cemetery wall adjacent to a busy street collapsed in Kurtuluş neighboorhood of Şişli district, wounding at least two people.
A fire erupted after a lightning stroke a depot in Kağıthane district.
The municipality previously warned that on average 50 millimeters of rain would fall.
Many buildings and offices were flooded as hailstones as big as paintballs shattered windows of cars and residential buildings.
