The Met Office warned of possible transport disruption and advised commuters to be extra careful of surface water during this morning’s rush hour.
Last night forecaster said that a number of homes and businesses could be in danger of being flooded. Fast-flowing or deep water possible, causing “a danger to life”.
Roads and train and bus services could also be disrupted.
The Met Office issued two yellow warnings of rain yesterday.The first for most of central and southern Scotland and northern, eastern and south-eastern England.
Previously set to cover an 18-hour period, the warning has been shortened after heavy overnight rainfall north of the border.
In Islay, in the Inner Hebrides, 55.6mm fell in the last 24 hours. Scotland’s central belt and the south of Scotland saw approximately 20mm of rain during that timescale. Meanwhile, in northern England some areas saw around 20mm of rainfall.
The Met Office said Cromer on the Norfolk coast saw the highest total rainfall in the past 12 hours with 46.4mm.
The Scottish Environment Protection Agency issued four flood warnings - meaning that flooding is imminent - and 11 flood alerts, giving an early indication of potential flooding from rivers, the sea and surface water, yesterday highlighting on their website that further heavy rain was expected today.
The flood warnings were for Romanno Bride to Lyne Station in the Scottish Borders; Innerpeffray to Bridge of Earn and Carse of Lennoch to Lochlane in Perthshire and Crieff to Innerpeffray, in Perth and Kinross.
Police forces across the country have taken to social media to warn drivers of standing water on the roads.
A Met Office spokeswoman said: “The weather in Scotland will be unsettled through the week. Monday will see a wet and windy start to the day across Scotland. This is coming from an area of high pressure across the north of the UK. The day will start off wet in the west moving to the east. It will be quite persistent with a lot of water in the roads during the rush hour.”
Flooding on the railway meant Greater Anglia services were unable to run between Norwich, Lowestoft, Great Yarmouth and Sheringham.
Customers were being advised not to travel on these routes, with a small number of rail replacement bus services put in place.