In Edinburgh, trains in and out of the city to be halted and streets were turned into rivers when the downpour hit. Images on social media showed multiple streets awash with rain which also crept into homes, bars, and businesses.
Emergency services attended some incidents including under one bridge in Chesser, where the Scottish Fire and Rescue Service could be seen helping vehicles which were stuck in the flooding.
Sunday’s stormy weather also caused a problem for shoppers in the brand new St James Quarter, which only opened last month.
One Twitter user, Jamie Cunningham, pointed out “a couple of design flaws when it comes to rain”. Water could be seen dripping down windows and onto the balconies of the several floors to ground level.
At around 5.46pm, ScotRail tweeted to confirm trains between Helensburgh and Edinburgh would instead run between the coastal town “and Bathgate only” for safety reasons.
Buses were arranged to run from Edinburgh to Glasgow while Network Rail workers “set up pumps which are running and helping water levels to recede”.
The rail firm said the track had been cleared shortly after 8pm.
One of the worst hit areas was Edinburgh’s Stockbridge, where local businesses were forced to close on Raeburn Place.
Brenda Pearson, who owns Abacus Blinds and Curtains on the street, said: "It's absolutely devastating. There's some stock we will just have to bin - such as sample books that are £200 each.
"It's just a nightmare. We've been shut for so long over lockdown and now this. It's the last thing we need after being shut for so long.
"It went through the basement and everything down there is soaked. We're having to take stuff away to our house to see if we can get it dried out and salvage anything."
Mark Kennedy, owner of nearby printing shop, Print Sponge, was alerted to the flood by friends who sent him a video of water gushing down the street.
He said: "We don't open on a Sunday, so I was at home and a couple of friends sent me videos saying 'have you seen Raeburn Place?'.
"We just have to get on with it. I'll be shut for at least a couple of days."
For many business owners in Stockbridge, it was the second flood in less than a year, after heavy rain last summer flooded the basements under their premises.
Shoppers heading for the Braehead Shopping Centre in Renfrewshire meanwhile were delayed by flooding on the slip road from the M8 motorway. Just a few miles away, there were similar blockages on the same motorway at Glasgow Airport.
Traffic Scotland used its twitter feed to warn motorists to slow down and drive to the rapidly-changing conditions.
Alex Burkill of the Met Office said: ”These disruptive events were not unexpected. We have had a yellow weather warning out for thunderstorms moving north through Scotland all day Sunday.
“In fact, things are only going to get worse as we go into the evening and even overnight into Monday.
“There’s lots of activity in the atmosphere. Humid air carries lots of moisture, which is why we have seen some heavy bursts of rain.”