Flood waters covered roads blocking cars in the districts of Kartal, Maltepe and Pendik in the city's Asian quarter amid continuing rain, it said.
Firefighters were called in to drain the overflow in hopes of normalising traffic, usually snarled at the best of times, in this sprawling city of more than 12 million.
Rains also caused damage in the neighbouring provinces of Duzce and Sakarya.
Weather services forecast continued rain in the centre and northeast of the country on Tuesday.