A yellow weather warning was issued for Fife and Tayside on Friday and is repeated for Sunday.
A Met Office spokesman said: “A moist and increasingly unstable airmass will affect Scotland with the likelihood of some heavy, thundery showers breaking out.
“These have potential to produce some large rainfall totals in a short space of time, leading to localised surface water flooding, whilst other nearby locations see very little.”
The public were warned to be aware of localised flooding and disruption to road and rail transport.
The inclement weather is caused by the remains of Hurricane Bertha making their way across the UK.
While most of the power of the hurricane has been dispersed as it travelled across the Atlantic, the weather is set to be “unseasonable”.
In a repeat of yesterday’s conditions, heavy rain is set to sweep in on Sunday causing disruption.
The Met spokesman added: “Given the unseasonable nature of the weather, this could be sufficient to disrupt transport and make outdoor activities dangerous.
“There continues to be a great deal of uncertainty in the forecast but the public should be aware of the risk of flooding due to heavy rain as well as very strong winds and large waves.
“There is the potential for rainfall totals of more than 50mm in places and coastal gusts of over 60mph.”