Updated at 6.20pm
Water levels rose in the Tal-Barrani area as rain water gathered there during Monday's storm - but they never reached alarming stage, the Traffic Control Centre said.
Some cars were caught unawares there at one stage, according to social media.
The centre, which monitors major roads by webcam, said that traffic was flowing at 2.40pm and that attention had turned to Msida, where the storm was heading.
A motorist in Luqa told the Times of Malta roads there were practically flooded by 3.15pm. Photos posted on social media showed water had also accumulated in Birzebbuga and Marsaxlokk.
The storm was, however, extremely localised: as it poured down in Luqa, roads in Marsa and Qormi were still dry.