At least six people have died and another six remain missing after Tropical Storm Wipha skirted the country on Friday, according to the National Disaster Risk Reduction and Management Council.
Many neighbourhoods in Manila woke to find calf-deep pools of floodwater Tuesday after an overnight downpour swelled the Marikina River.
More than 23,000 people living along the riverbank were evacuated from their homes overnight and moved to schools, village halls and covered courtyards.
About 47,000 more were evacuated from across the capital's Quezon, Pasig and Caloocan areas, as well as from the main government district.
"Usually, these people are from low-lying areas like beside creeks," said Wilmer Tan of the Marikina rescue office, who said the river had reached 18 metres (59 feet) in height.
An elderly woman and her driver were swept down one of the swollen creeks as they attempted to cross a bridge in Caloocan, said John Paul Nietes, an emergency worker.
It was initially hoped that the pair had escaped after the car was recovered with a broken window.
But Caloocan Mayor Dale Gonzalo Malapitan announced one of the bodies had been found.
"We've found (the driver)," he told Manila radio station DZMM.
"The body was recovered 4.5 kilometres from where the vehicle was swept away.... They were unable to bail out."
- No respite -
As floodwaters began receding in Manila by Tuesday afternoon, the national weather service said a low-pressure area off the country's east coast had developed into a tropical depression.
While not expected to make landfall, the depression would bring continued heavy rain through the end of the week, the agency said.
Thousands of people, meanwhile, remained unable to return to their homes.
AFP journalists in Cainta, a small town on the outskirts of the capital, saw residents using styrofoam boxes and abandoned refrigerators as makeshift floatation devices to navigate the floodwaters.
Angelo Dela Cruz, 18, employed a rubber boat -- one purchased in anticipation of frequent flooding -- to transport rice for his aunt's small eatery.
"Instead of using the van, we have to use the boat and push it while we wade through the flood to prevent the rice from getting wet," he said.
At least 20 storms or typhoons strike or come near the Philippines each year, with the country's poorest regions typically the hardest hit.
Deadly and destructive storms are becoming more powerful as the world gets warmer because of climate change.
"This is hard, because if the rain will continue... the river will swell," Manila street sweeper Avelina Lumangtad, 61, told AFP as she stood next to a flooded thoroughfare.
"The floods are dangerous."
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