Two elephants also drowned in rapidly rising flood waters north of the city, their sanctuary said Sunday.
In the centre of Chiang Mai, people waded through brown floodwaters in the night bazaar, and water flowed into the central train station, which has now been closed.
Local media reported that thousands of bed-ridden elderly and children were in need of food and evacuation after the Ping River reached an historic high on Saturday night.
By Sunday, the water level had receded slightly, authorities said.
Saritdet Charoenchai, a public health official, said that three people had been killed, including a 44-year-old man who was electrocuted and a 33-year-old woman who died in a "mudslide".
More than 80 people have moved into shelters, he said, as almost a dozen medical centres were closed due to the high water, he added.
A local TV station showed a monk carrying a coffin through floodwaters to a cremation site.
In Mae Tang district, more than 100 elephants at the Elephant Nature Park in Chiang Mai province were moved to higher ground to escape rapidly rising flood waters, an employee who gave her name as Dada, told AFP.
But two elephants -- named in local media as 16-year-old Fahsai and 40-year-old Ploython, who was blind -- were found dead on Saturday.
"My worst nightmare came true when I saw my elephants floating in the water," Saengduean Chailert, the director of the Elephant Nature Park in northern Thailand, told local media.
"I will not let this happen again, I will not make them run from such a flood again," she said, vowing to move them to higher ground ahead of next year's monsoon.
Major inundations have struck parts of northern Thailand as recent heavy downpours caused the Ping River to reach "critical" levels, according to the district office.
Thailand's northern provinces have been hit by large floods since Typhoon Yagi struck the region in early September, with one district reporting its worst inundations in 80 years.
While Thailand experiences annual monsoon rains, man-made climate change is causing more intense weather patterns that can make destructive floods more likely.
Twenty of Thailand's 76 provinces are currently flooded, the Department of Disaster Prevention and Mitigation said Sunday.
Flash flooding kills three in northern Thailand
Flash flooding in popular Thai tourist hotspot Chiang Mai has killed three people, a health official said Sunday, as visitors evacuated hotels through knee-high muddy water and shops closed in the city centre.
Flash flooding in popular Thai tourist hotspot Chiang Mai has killed three people, a health official said Sunday, as visitors evacuated hotels through knee-high muddy water and shops closed in the city centre.
Residents transport their motorbike through a flooded street in Chiang Mai, on October 6, 2024.