Heavy rain overnight has caused schools and roads to be closed across Egypt.
Storm conditions, which began in the south on Saturday, reached Cairo and Giza on Sunday night.
At least 16 people have been killed across Egypt over the past 48 hours due to heavy rain and storms.
Meteorological authority chief Ahmed Hussein said the weather would remain unstable until Thursday.
Sand and rain storms are expected to hit the Red Sea and Mediterranean coasts on Wednesday, he predicted. Visibility could be difficult and some ports might be closed.
Flooded streets added to traffic congestion in parts of the capital on Monday morning.
A rock fell from Moqattam hill early Monday, blocking traffic for several hours, state-owned Radio Misr reported.
The Hurghada-Cairo and Qusayr highways were closed due to the bad weather, the interior ministry said.
Some schools in the Red Sea governorate were closed on Monday due to heavy rain, especially in Hurghada.
The international arrivals hall at Hurghada airport was damaged by rain on Sunday, forcing passengers to be moved to the domestic travel terminal.
In South Sinai, Nuweiba suffered a complete blackout when electricity was cut to prevent a short circuit.
In Upper Egypt, Assiut governor Ibrahim Hamad announced the closure for two days of thirty schools in areas hit by storms.
In the Nile Delta, villages and cities in Kafr El-Sheikh governorate suffered heavy rain for almost three hours on Sunday. The ports of Rashid and El-Bourlos were closed as a result. Fishing activities were also halted in the Mediterranean Sea, Rashid and El-Bourlos lake.
Electricity was cut off in hundreds of villages in Kafr El-Sheikh.