Around two weeks' worth of rain fell in just a few hours causing chaos across Glasgow, Ayrshire, Renfrewshire and the Borders.
Two so-called mini tornadoes were reported in the south while lightning brought down communications at council headquarters in Dumfries.
Firefighters battled to rescue the worker in Kilmarnock, who was contracted to work for Scottish Water, as he clung on to his JCB cabin for 45 minutes around 3.30pm yesterday.
He was eventually rescued by boat, while his colleague, who was on the riverbank, was saved by fire crews.
Owen Hanratty, Group Commander, said: "The first worker was rescued from the riverbank by fire crews using an extension ladder.
"However, a suitable launch site had to be identified as the second worker required to be rescued by boat.
"Both workers were assessed by paramedics at the scene, but were found not to have sustained any injuries."
In Galston, East Ayrshire, six people had to be rescued from their homes after flash flooding hit the town.
Residents of five properties in Wallace Street and Barr Street were led to safety shortly before 4pm.
In Jedburgh, a clean-up operation, led by residents and businesses owners, was under way to try to clear up the damage following extensive flooding.
The mini-tornadoes were spotted at Annan and another near Dalbeattie yesterday.
A Met Office spokesman said: "Such funnels are not uncommon in thundery and wet weather. It is only classed as a tornado if they touch earth."
The sun is expected to make a belated appearance towards the end of this week across Glasgow and the West – with temperatures set to peak at around 20°C.
Sepa put in place flood alerts for 10 regions yesterday and the Met Office said yellow alerts for heavy rain continue today in Orkney and Shetland, Highlands and Islands, Grampian, Strathclyde, Central, Tayside and Fife, South-west Scotland and Lothian Borders.