The Met Office recorded 117.4 mm of rainfall till 8.30 am on Saturday.
"Spells of rain and thundershowers are expected during the day," a Met official said.
While people waded through knee-deep water, public transport refused to ply in various parts of the city.
Slum-dwellers near Kankurgachi and Ultadanga in east Kolkata battled the inclement weather with layers of tarpaulin sheets and plastics woven around their huts but the inundation has left them in dire straits.
"Even if we protect the roof by layers of plastics, water enters in due to the rains," a dweller in Duttabad slum near Kankurgachi said.
Water-logging also forced members of many family residing on the ground floor in duplexes to move up to the upper storeys.
"When I woke up this morning (Saturday), water had reached up to the foot of my bed. I have decided to shift to the upper floor," C. Talukdar, a senior citizen residing in Salt Lake here, told IANS.
Meanwhile, the death count in West Bengal flood has gone up to 39, with many areas in six districts still water-logged, Chief Minister Mamata Banerjee.
The chief minister said stretches in Burdwan, Birbhum, Hooghly, Howrah, North 24 Parganas and South 24 Parganas districts were submerged.