The river on the Noto Peninsula -- an area still reeling from a devastating earthquake in January -- overflowed at the weekend, becoming a muddy torrent that inundated roads and a remote hamlet.
After the skies finally cleared, police and firefighters from across Japan were joined by residents and the father of a 14-year-old girl who is one of seven missing people.
The number of deaths reached seven, with one severely injured and 11 mildly injured as of Monday afternoon, Ishikawa prefecture said on their website.
Rain pounded the region from Saturday, with more than 540 millimetres (21 inches) recorded in the city of Wajima over 72 hours -- the heaviest continuous rain since comparative data became available.
The flooding disaster hit the area as it was making a fragile recovery from a magnitude-7.5 quake on New Year's Day, which toppled buildings, triggered tsunami waves and sparked a major fire.
Floodwaters inundated emergency housing built for those who had lost their homes in the January 1 earthquake, which killed at least 374 people, according to the Ishikawa regional government.
"I have to start over, through another cold winter," 76-year-old former sushi chef Shoichi Miyakoshi, whose wife was killed in a 2007 earthquake, told AFP.
On Monday afternoon, 3,600 households still had no power after the rain, according to the Hokuriku Electric Power Company.
More than 100 areas in the region were isolated, with roads blocked due to landslides.
- 'I want to hug her' -
In Wajima, one of the cities worst affected by the recent earthquake, dirty puddles and piles of branches covered the streets.
Widespread evacuation orders were in place over the weekend but several residents returned to clear the mud.
Takaya Kiso, the father of the missing 14-year-old, told TV Asahi and other local media that he hopes she will be found soon, as "I want to hug her".
His daughter "was asleep so she wasn't aware of the situation. She woke up because of my phone call. When she looked outside, it was like a sea, with floodwater covering roads," he said in Wajima.
But when Kiso rushed back from work, the house was gone, the reports said.
Akemi Yamashita, a 54-year-old Wajima resident, told AFP she had been driving on Saturday when "within only 30 minutes or so, water gushed into the street and quickly rose to half the height of my car".
"I was talking to other residents of Wajima yesterday, and they said, 'It's so heartbreaking to live in this city'. I got teary when I heard that," she said, describing the earthquake and floods as "like something from a movie".
"I can't help thinking the Noto region might be cursed or something."
Scientists say human-driven climate change is intensifying the risk posed by heavy rains because a warmer atmosphere holds more water.
The areas under the emergency warning saw "heavy rain of unprecedented levels", a weather agency forecaster had warned on Saturday, advising people to "secure your safety immediately".
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