Several main roads in the center of Thessaloniki became flooded due to strong downpours on Tuesday morning and parts of the northern port city were left without electricity as storms knocked out power lines.
Imathia, Pella and Katerini, also in northern Greece, also experienced heavy downpours.
The summer storms are expected to spread through the country on Tuesday, moving south to reach Athens around midday.
The National Hellenic Meteorological Service said that the showers may be accompanied by hail and lightning and warned holidaymakers to leave beach locations in the event of a storm.
It said the northern Aegean should brace itself for strong winds with sailors taking special care, and added that the islands of the Ionian should also expect plenty of rain over the course of the day.
The wet front will become restricted to eastern and northeastern parts of the country on Wednesday, the service forecast.