MMDA said parts of the Epifanio de los Santos Avenue (Edsa) were flooded.
It said Gutter-deep flood hit Edsa Centris northbound in Quezon City and was not passable to all types of vehicle.
Flooding was also reported along Edsa White Plains in Quezon City and Edsa Tramo in Pasay City.
The northbound lane of C5 along Tiendesitas in Pasig City was not also passable to all types of vehicle.
Gutter-deep flood also hit C5 Libis in Quezon City while knee-deep flood swamped Katipunan Avenue in the vicinity of Ateneo de Manila University.
Gutter-deep flood was also reported in C5 Greenmeadows and Ortigas.
Parts of Commonwealth Avenue in Quezon City were also flooded.
The Edsa corner Quezon Avenue and Balara along Commonwealth Avenue are not passable to all types of vehicle.
Gutter-deep flood also hit the stretch of the Congressional Avenue.
Other flooded areas in Quezon City include the Araneta Avenue, Quezon Memorial Circle, Road 1, in Project 6.
In Manila, España Boulevard and Taft Avenue were also swamped with flood.
MMDA has lifted the number coding scheme on Friday except in Makati and Las Piñas.