Two people were reportedly drowned in floods and several flights were delayed as Mumbai received heavy monsoon showers for the third successive day, triggering fears of a repeat of last year's flooding.
The men drowned in Thane's Kashimira area.
Rains flooded homes, submerged rail lines and forced people to wade through muddy streets in India's financial capital.
The drainage system once again struggled to cope with the downpour, prompting civic workers to use spades and crowbars to open clogged manholes.
"Our locality looks like a sea. There is knee-deep water. Rainwater is entering many houses," Sylvester Nato, a resident of Bandra, said.
The downpour inundated several roads in central and northern Mumbai and rainwater submerged rail tracks at some places. Air services were also running late.
Last year, two days of heavy rain exposed the city's poor infrastructure and dismal emergency response in India's richest city.
The floods killed people in and around Mumbai and shut down the city for almost a week.
"We have reports of some low-lying areas being flooded. But we are much better prepared this time," said Maharashtra Chief Minister Vilasrao Deshmukh.
Weather officials forecast heavy to very heavy rains in the next 48 hours, prompting civic authorities to check drainage systems, traffic management and the suburban railway network.
"There are some reports of water-logging in some areas, but we are working to clear those roads," said Johny Joseph, Mumbai's chief civic official.