Local showers and brief storms are forecast on Sunday in parts of the Greek capital, the Peloponnese, the central and eastern mainland, Evia, Thessaly, the Sporades islands and Macedonia.
The National Meteorological Services said the islands of the northern and eastern Aegean may also see some rain, with conditions easing from the west overnight.
A state of emergency, meanwhile, was declared in Megalopoli in the central Peloponnese, which was lashed by heavy rains on Saturday.
Authorities there said that flood damage to private and public property is quite extensive as the area saw around 190 centimeters of rain in seven hours.
Peloponnese Regional Governor Petros Tatoulis chaired an emergency meeting with local authorities in Megalopoli to discuss an assessment of the damage. On Monday, he will meet with civil protection authorities in Athens in order to begin restoration procedures.
In the regional capital, Tripoli, a storm knocked out power lines, plunging the town into darkness for several hours on Saturday, while some 1,000 people were safely evacuated from an events hall after the roof collapsed under the weight of the rain.
Holidaymakers are advised to stay away from the sea in the event of lightning and strong winds until skies clear.
Motorists should also avoid driving in heavy rain as visibility may be limited.