All three deaths were reported from Thiruvananthapuram district which received copious rains since this afternoon, police said.
Low-lying areas were waterlogged and the collector has asked people living in such areas to be cautious.
Onward journey of several trains, including Rajdhani Express, have been delayed due to waterlogging at the railway station here, railway sources told PTI.
Due to the flooding of roads, traffic was held up in various parts of the city.
According to Met office, heavy rains were also reported from Alapuzha, Punalur and Kottayam areas.