Just before the morning rush hour, more than 300 mm (11.8 inches) of rain lashed the city of 12 million over the six hours until 7:00 a.m (0130 GMT), municipal officials said, with more heavy showers forecast later in the day.
Commuters waded through knee-deep water that partially submerged vehicles in many areas, as traffic piled up on the city's Eastern and Western Express highways.
Water on the tracks forced railway authorities to cancel some long-distance trains, they said, while television images showed some suburban passenger trains, a critical means of daily transport for millions, halted on inundated lines.
More than 250 flights were delayed and at least 30 cancelled at the city's airport, the website of tracking service Flightradar24 showed.
The heavy downpour came days after record-breaking showers in the capital, New Delhi, that caused the fatal collapse of an airport roof.
Torrential monsoon rains have triggered floods and landslides in India's north and east, as well as in the neighbouring Himalayan nation of Nepal, where at least 11 people were killed.
More than 2 million people have been affected by rivers flooding in northeastern Assam, where the Kaziranga National Park, home to the rare one-horned rhinoceros, was inundated with six of the animals drowned, authorities said on Sunday.
State authorities said 66 people have died in floods and rain related incidents since May.
Flooding has also affected 31 villages in India's most populous state of Uttar Pradesh on the Nepal border, the state government said.
