Several governorates witnessed light rain early Wednesday, according to Egypt's Meteorological Authority.
Alexandria witnessed light rain earlier Wednesday, but its port remained open, according to the state-owned MENA news agency.
Light rain on Cairo and Giza disrupted traffic in various areas, but no accidents were reported.
Earlier this week, the Meteorological Authority warned that of unstable weather conditions in different parts of the country on Tuesday.
The traffic department at the ministry of interior advised drivers to drive cautiously and reduce speed on highways because of the rain.
The coastal city of Kafr El-Sheikh, in the north Delta, also saw light rain since Tuesday evening.
Port Said on the Suez Canal witnessed light rain on Wednesday morning.
The Meteorological Authority forecast on Wednesday thunder and rain for the northern coast, and rain for Cairo, the Nile Delta governorates and Suez Canal cities.
A decrease in temperatures is expected all over the country.
The Mediterranean Sea will be see high waves according to the authority's statement, but the Red Sea that will be more stable for navigation.
Cairo is expected to witness on Thursday a high of 20 degrees Celsius with a relatively cold low of 15 degrees Celsius.
Alexandria will see a high of 20 ºC and a low of 13 ºC.