Roads in some low-lying areas like Hindmata, King's Circle and Kalachowki were inundated after heavy rainfall during the night.
Heavy rainfall has triggered water logging in parts of Mumbai.
According to the Brihanmumbai Municipal Corporation (BMC), rain intensity has reduced and there is no waterlogging anywhere in the metropolis.
In a series of tweets, Maharashtra Aaditya Thackeray said parts of Mumbai have received over 83 per cent of the annual normal September rainfall in less than 12 hours.
With waterlogged tracks, suburban services of both Central Railway and Western Railway were suspended early Wednesday morning.
Mumbai and neighbouring areas received intense spells of rain since Tuesday night, leaving many parts of the metropolis in waist deep water and disrupting rail and road traffic.
Heavy showers overnight and early Wednesday morning caused waterlogging at many places in the metropolis, disrupting rail and road traffic.
The bail pleas filed by actress Rhea Chakraborty and her brother Showik Chakraborty, both arrested in a drugs case related to the death of actor Sushant Singh Rajput, were to be heard on Wednesday.
On Wednesday morning, public transport services were hit and normal life affected in the financial capital due to heavy downpour and waterlogging.
The India Meteorological Department (IMD) official added that an 'orange warning' (indicating heavy to very heavy rainfall) has been issued for the Vidarbha region for the next 48 hours.
Mumbai and neighboring Thane district received widespread moderate to heavy rainfall over the 24-hour period ended at 8:30 am on Friday.
A brown alert of heavy to very heavy rainfall has been issued for Raigad, Nashik and Pune, an IMD official said.
While Mumbai is expected to receive light to moderate showers, neighbouring districts of Thane, Palghar, Raigad and Ratnagiri may witness heavy rains at isolated places.
Heavy rains and gale had lashed Mumbai and neighbouring districts on Wednesday.
Massive flooding in Mumbai again shows that the frequency of localised heavy rain has increased during 1951–2017, with 285 reported flooding events in India during the period.