Rosario Brutas, a market vendor in Bacoor, a town south of Manila, said she and her husband woke on Tuesday to discover their home already partly submerged.
"We woke up before dawn to find our bed afloat," the 32-year-old told AFP from a hospital courtyard where her family and their neighbours had taken refuge.
Bad weather from seasonal southwest monsoons has pounded Manila and nearby areas for over a week since Typhoon Saola brushed past the country's north.
Before the latest deluge, the death toll from eight days of sustained rains had reached 53 with more than 268,000 people forced to flee their homes across the country, according to disaster authorities.
No new casualties were reported from the overnight rains.
But Jean Navarez from the state weather service warned that the floods could worsen as the La Mesa dam, Manila's sole reservoir, began letting off water that would swell surrounding rivers.
"If we put it in a percentage, at least 50 percent of Metro Manila is flooded," she told AFP.
"There will be heavy rainfall for the next 24 hours. The floods will increase," she added.
Government weather forecaster Bernie de Leon said that in the 24 hours to Tuesday morning, 323 millimetres (13 inches) of rain fell on the capital, compared to average monthly rainfall of 504 millimetres for August.
The National Disaster Risk Reduction and Management Council said that while some 20,000 people fled to evacuation centres overnight, many more sought refuge in relatives' homes.
The La Mesa dam overflow and a high tide on Manila Bay conspired to worsen the flooding, it said.
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