The torrential rain showers moved in from the south with no warning, with the deluge blocking roads and trapping cars and buses in the water, local police say.
All buses in Malmö were cancelled, after over 20 got stuck in the water. Services will resume once the floodwaters have drained away, local bus company Skånetrafiken told news agency TT.
Around 3000 people also lost electricity when substations in the area were also flooded, several motorways in the area are also closed due to the water levels.
Over one hundred emergency calls have been made to the emergency services, according to the local Sydsvenskan newspaper.
The Swedish weather service SMHI has updated its forecast and has now issued a class one weather warning for more heavy showers in western Skåne. The class one warning is the lowest in the three point warning system.
88 millimetres of rain fell in Malmö between 2am and noon, a month's worth, according to SMHI.
Train services on the other side of the Öresund, in Copenhagen, have also been hit by the bad weather.