Two young girls -- reportedly aged four and one -- were missing after possibly being swept away by floodwaters in the wake of Friday's storm.
The deluge left hospital rooms underwater, turned neighborhoods into islands and cut electricity to swaths of the city. National Security Minister Patricia Bullrich said Bahia Blanca was "destroyed."
The death toll rose to 13 on Saturday, up from 10 on Friday, authorities said.
The mayor's office said more casualties were possible in this city of 350,000 residents, located 600 kilometers (370 miles) southwest of the capital Buenos Aires.
The missing girls "may have been carried away by the water," Bullrich told Radio Mitre.
At least five of the victims died on flooded roadways, possibly after being trapped in their cars by fast-rising water.
The downpour, which began Friday morning, dumped more than 400 millimeters (15.7 inches) of rain in the area in just eight hours, "practically what Bahia Blanca gets in an entire year," provincial security minister Javier Alonso said.
"This is unprecedented," he added.
Tempers flared Saturday as Bullrich and Defense Minister Luis Petri tried to visit an affected neighborhood, with residents complaining they should have visited the area the previous night, according to a video shared on social media.
Some locals tried to drag Bullrich toward floodwaters, shouting "get wet!" and other abuse, before she was pulled away from the scrum by police and government officials.
For environment official Andrea Dufourg, the extreme weather event "is a clear example of climate change."
"Unfortunately this will continue to take place... we have no other option than to prepare cities, educate citizens, establish effective early warning systems," said Dufourg, who is director of environmental policy for the city of Ituzaingo outside Buenos Aires.
The number of evacuees on Saturday stood at 850, down from a peak of 1,321, according to the mayor's office.
- Babies evacuated -
The storm forced the evacuation of Jose Penna hospital, with news footage and video shared on social media showing nurses and other medical staff carrying babies to safety. They were later assisted by the army.
Nearly 1.5 meters (five feet) of muddy water gushed into doctor Eduardo Seminara's office.
"Everything is ruined," he told local channel C5N, pointing to a pile of soggy chairs, cushions and books dumped on the sidewalk.
But "I'm not complaining, we didn't lose any lives, our family is fine," he said.
Local media showed images of flooded shops and reported overnight looting.
The government has authorized emergency reconstruction aid of 10 billion pesos ($9.2 million at the official exchange rate).
The storm left much of the surrounding coastal area without power. At one point, city officials in Bahia Blanco suspended electricity due to the huge amount of water in the streets.
Bahia Blanca has suffered past weather-related disasters, including a storm in December 2023 that claimed 13 lives. It caused houses to collapse and provoked widespread infrastructure damage.
Heavy rains also fell Friday night in the resort town of Mar del Plata, with officials suspending evening activities and urging people to remain indoors.
Buenos Aires was also hit by the storm but suffered no major damage.
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