Images on social media showed a torrent of muddy water sweeping cars and rubbish bins from the streets in Safi, which sits around 300 kilometres (186 miles) south of the capital Rabat.
At least 70 homes and businesses in the historic old city were flooded, authorities said.
Another 32 people were injured and taken to hospital, but most of them have been discharged.
Damage to roads cut off traffic along several routes to and from the port city on the Atlantic coast.
"It's a black day," resident Hamza Chdouani told AFP.
By evening, the water level had receded, leaving people to pick through a mud-sodden landscape to salvage belongings.
Another resident, Marouane Tamer, questioned why government trucks had not been dispatched to pump out the water.
As teams searched for other possible casualties, the weather service forecast more heavy rain on Tuesday across the country.
Severe weather and flooding are not uncommon in Morocco, which is struggling with a severe drought for the seventh consecutive year.
The General Directorate of Meteorology (DGM) said 2024 was Morocco's hottest year on record, while registering an average rainfall deficit of -24.7 percent.
Moroccan autumns are typically marked by a gradual drop in temperatures, but climate change has affected weather patterns and made storms more intense because a warmer atmosphere holds more moisture and warmer seas can turbocharge the systems.
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