Storm Henry, which forced the cancellation of classes in some areas, made landfall before dawn in Fuga Island in Cagayan.
The tropical storm is now heading to the West Philippine Sea, according to PAGASA meteorologist Chris Perez.
An orange yellow rainfall warning, which is the second highest in a 3-step alert system, was raised at 7.30am over Metro Manila, Bulacan, Bataan, and Batangas areas.
The Philippine Atmospheric Geophysical and Astronomical Services Administration (PAGASA) added floods are threatening these areas.
The yellow warning rainfall alert was up over Rizal, Cavite, Pampanga, and Zambales, where floods may swamp low-lying areas, the weather agency said.
Manila is already feeling the effects of the storm, after the water level in Marikina River reached 16.6 meters above sea level at 4pm local time.
This prompted local officials to raise the second alarm, as residents near the river automatically are asked to evacuate once the water level reaches 16 meters.
Once the water level reaches 18 meters, the local government’s disaster response unit will be forced to implement forced evacuations of people living along the river.
Residents are also advised to monitor the water level and stay alert.
Waist-deep and knee-deep floods have been reported in some areas.
This caused problems for commuters on their way to work this morning.
The Philippine National Railways cancelled and delayed trains.
Airlines also canceled flights due to the bad weather.
PAGASA added at least two more storms are expected to enter the Philippines in July.
Last week, Typhoon Gardo brought heavy rains to the western sections of Luzon and Visayas.