East Lothian, Edinburgh Midlothian Council, the Scottish Borders and West Lothian have all been upgraded to an amber weather warning of thunderstorms.
It comes as a yellow warning was issued across Scotland for Tuesday into Wednesday.
A yellow warning of rain is also in place across the Capital and other areas.
The Met Office has said that this amber warning of thunderstorms will be in place for the affected areas from 12pm on Tuesday until 10pm the same day.
A Met Office spokesperson said: “Showers will break out widely across much of Scotland from late morning, turning heavy in the afternoon.
"While many places will miss the heaviest showers, where they do occur 20-40 mm could fall in an hour with locally 60-80 mm in a few hours.
"Showers will start to merge to longer spells of rain in the evening, but easing in intensity.”
Other regions and local authorities affected include Clackmannanshire, Falkirk, Fife, Perth and Kinross, Stirling, Grampian, Aberdeenshire, Moray, the Highlands, Argyll and Bute, East Dunbartonshire, North Lanarkshire and South Lanarkshire.
A yellow warning will remain in place across the amber warning affected areas and more areas including Glasgow from 12pm today till midnight.
Under the warnings, flooding of homes and businesses is possible and could happen quickly, with damage to some buildings from floodwater, lightning strikes, hail or strong winds.
Delays and some cancellations to train and bus services are likely and spray and sudden flooding will probably lead to difficult driving conditions and road closures.
Amber warnings even include possible risk to life and property.
After recent flooding at the St James Quarter, measures have been taken to mitigate this happening again.
A St James Quarter spokesperson said: “We have now completed works to resolve the flooding issues that occurred earlier this month and a robust interim mitigation system is in place, with the final storm water mitigation system at St James Quarter due to complete in the coming months.”
Edinburgh City Council has also said officers will be on standby, and will be monitoring the culvert grilles and rivers if there is significant rainfall.
Responses could include clearing blocked culverts or closing flood gates.