The Tulsi lake -- a major source of water supply for the city and its suburbs -- overflowed due to the heavy showers.
Mumbai's famous tiffin carriers Dabbawalas, also suspended their services today.
The India Meteorological Department (IMD) has predicted heavy to very heavy rain till Thursday.
The IMD's Colaba observatory (for Mumbai) recorded 165.8 mm rainfall in the 24-hour period of 8.30 am yesterday till 8.30 am today.
The Santacruz observatory, which records rainfall for suburban Mumbai, reported 184.3 mm rainfall in the same period.
Since last night, over 200 mm rainfall has been recorded and this has led to waterlogging on rail tracks, a railway official said.
Keeping in view the safety of passengers, services on the fast track between Vasai and Virar in Palghar district and that of the air-conditioned local trains have been suspended till the water level on tracks recedes, he said.
"Services of AC local have been suspended today in view of very heavy rains & water logging at/around Nallasopara, till further information," the Western Railway (WR) said in a tweet.
"Water very high from rail level at Nallasopara following heavy water accumulation in adjoining areas of tracks. Rail traffic suspended bet (sic) Vasai Road - Virar. Trains running between Churchgate & Vasai Road with delay," the WR said in another tweet.
However, the slow track services were operational between Churchgate in south Mumbai and Virar. Trains were running late by 10 to 20 minutes, the railway official said, adding that pumps were being used to drain out water from tracks.
In view of the flooding on rail tracks, the WR terminated and cancelled nine outstation trains, he said.
Arrangements were being made to provide snacks and water to passengers of the long-distance trains that were delayed or stopped at various stations, the official said.
The Central Railway's local train services on its main and harbour lines were running late by 15 to 25 minutes, a CR official said.
Three inter-city express trains were also cancelled, he said.
Meanwhile, Dabbawalas suspended their tiffin delivery services due to the rough weather.
"We did not collect tiffins today because of the water-logging across the city. Our people were finding it hard to wade through knee-deep water on their bicycles," Mumbai Dabbawalas' Association's spokesperson Subhash Talekar said.
A Defence spokesperson said, "Our (Navy) rescue, diving and air teams are on standby. No assistance has been sought so far."
There were reports of waterlogging form several areas, including Hindmata, Parel, King's Circle, Dharavi, Kurla, Sion, Bhandup, Vikhroli, Mulund, Dadar and Borivili, a BMC disaster management unit official said.
"Vehicular movement was slow on the Western Express Highway. However, traffic movement on the Eastern Express Highway was normal," he said.
Brihanmumbai Electric Supply and Transport (BEST) buses on 14 routes were diverted, a BEST spokesperson said.
Maharashtra Education Minister Vinod Tawde has asked school principals here to decided if institutions need to be kept open today.
"Instructed Deputy Director to ensure that schools in Thane and Palghar districts remain closed due to the erratic weather conditions.
"In Mumbai, the principals of schools are instructed to take the call on school closure, gauging the water logging in the adjacent areas," Tawde tweeted.
The Brihanmumbai Municipal Corporation (BMC) has asked people not to believe in rumours, doing rounds on the social media, of a cyclone approaching the city.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)