Flooding early Tuesday morning killed at least 46 people in the city of La Plata and caused six deaths in nearby Buenos Aires. Many neighborhoods in both cities were still flooded and without electricity Wednesday.
Buenos Aires province Gov. Daniel Scioli said the death toll in the provincial capital La Plata could increase.
"I'm deeply saddened to say there are 46 victims that have been found so far," Mr. Scioli said in a televised interview Wednesday afternoon.
La Plata and the surrounding municipalities are home to about 1.7 million people.
State news agency Telam reported that as much as eight inches of rain fell in some areas of the city.
Sergio Berni, the No. 2 official in the federal Security Ministry, said that personnel from the army, coast guard and other security forces have been deployed to evacuate stranded La Plata residents.
"Half of La Plata is flooded," Mr. Berni said.
Television channel TN broadcast footage showing vast swaths of the city covered by flood waters and rescue workers using boats to get to people stranded in their homes. Telam said 2,200 people have been evacuated so far.
President Cristina Kirchner visited a stricken La Plata neighborhood in a helicopter, where she met with residents.
"We are bringing [Army] field kitchens to provide hot food and we are going to bring water purification [equipment]," she said.
The capital of Buenos Aires, located about 35 miles to the northwest of La Plata and home to around 2.9 million residents, also was struggling to recover from the storm that dumped more than seven inches of rain in some parts of the city.
In low areas of the city, the depth of the flood waters exceeded three feet, while some streets and avenues in middle-class districts were turned into raging rivers that swept away cars and people.
Mayor Mauricio Macri said it was the worst storm to hit the city since 1906.
The federal Planning Ministry said that about 272,000 people in the greater Buenos Aires urban area are still without electricity, down from about one million Tuesday morning.
Argentine state-controlled oil company YPF SA YPF -0.43% suspended operations at its La Plata refinery after a power outage Tuesday triggered a fire in a coking unit.
YPF said fire crews have contained the blaze, which no longer represents a risk to other part of the refinery.
A company spokesman said it is too early to quantify the damage and lost output.
Argentina is a major fuel importer, and the La Plata refinery supplies almost 30% of the country's domestically produced fuel.
Argentina's soybean and corn crops appear to have avoided significant storm damage, though the rain will likely delay the harvest.
Argentina is the world's No. 3 soy exporter and ranks first in exports of soyoil and soymeal. Farm exports are the South American country's single largest source of the foreign currency it needs to buy imported goods and pay its creditors.
Farmers were making good progress with the soy harvest, but wet conditions and boggy roads in Buenos Aires province are going to cause some delays, said the Buenos Aires Cereals. Exchange's chief agricultural analyst, Esteban Copati.
Up until now most analysts held a rosy outlook for the soy harvest, with the Agriculture Ministry expecting production to hit a near record 51.3 million metric tons, up 28% from last year.
Weather over the next week will be key. If the rain lets up, the harvest will get back on track within five days, Mr. Copati said.
But Mother Nature shows no signs of letting up. The federal meteorological agency expects accumulated rainfall of up to four inches Wednesday and Thursday in some areas of central and southern Buenos Aires province and the eastern part of neighboring Pampa province.
—Taos Turner and Shane Romig contributed to this article.
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