The rain passed through Gothenburg on the west coast and the Dalsland and Värmland regions on Tuesday morning before moving on to Norway.
But it was expected to return later on Tuesday, heading back via southern Sweden before reaching the Baltic Sea island of Gotland in the evening.
National weather agency SMHI issued an alert for heavy rainfall in the southern Skåne region, warning of thunderstorms and more than 35 millimetres of torrential rain in three hours.
Meanwhile, Stockholm was set for a fairly calm day with temperatures of up to 20C, and the northern Norrland region was also predicted to have a day of normal autumn weather.
SWEDISH WORD OF THE DAY: Skyfall
Rain in Malmö on Tuesday. Photo: Johan Nilsson/TT