In a climate disaster of epic proportions, the downpour washed away roads, homes and crops, killing some 1,700 people and displacing tens of thousands.
The government estimates the clean-up operation will cost Pakistan's struggling economy more than 30 billion dollars.
Survivors face waves of disease
For now, though, a more pressing concern is the inevitable surge in cases of malaria, dengue fever, gastric infections and other diseases.
According to the Directorate General of health services in Sindh, one of the worst-hit provinces, between July and the beginning of October almost 350,000 people were suspected of malaria, more than 700,000 had some form of diarrhea, and over 770,000 reported a skin-related ailment.
"Malaria cases are up because of the stagnant water, while the incidence of diarrhea is at least five times greater than normal," says Associate Professor Tufail Ahmed Soomro.
The Gulam Muhammad Mahar Medical Hospital where Soomro works is packed with patients.
In order to treat everyone, particularly children, staff have been forced to put three or even four patients in a single bed.
Momal brought her ailing four-year-old son to the hospital, only to be told that he had to share a bed with another child who was being treated for malaria.
As she holds her son to her chest, Momal describes how her family has been forced to live outdoors since their home was damaged by floodwaters.
Her fears grow as she sees an 8-month-old die in a nearby bed. The infant was admitted in the third week of September with a high fever and other symptoms of malaria. She eventually succumbed to pneumonia.
One doctor who spoke to NHK on condition of anonymity said that he recently returned to duty after being hospitalized for three days with malaria himself.
He said many other medical workers are also getting sick.
"Malaria is a serious concern. Every patient with a high fever is treated as a suspected case of malaria," says the doctor.
Outside the hospital, parents and guardians who can't afford accommodation have set up makeshift camps as they wait for family members to convalesce.
The provincial government says it may take three to six months before the floodwaters recede -- but there are many who will not be able to wait that long.
Another setback for farmers
Abdul Aziz Chachar is a farmer whose 500 or so acres of land have been passed down through his family across the generations.
He planted all of his fields with rice in hopes of a bumper crop after he lost half of his wheat in a heat-wave that struck in March and April.
The 59-year-old says his paddy fields should look green and ready to harvest about now. Instead, they are a scene of devastation.
"I have never experienced such torrential rain," Chachar told NHK.
His fields are still wet with stagnant water, though he has managed to pump away much of the floodwater to prepare for another sowing of wheat.
"The paddies are gone. I'm a farmer and I have to think about the future," he says.
"I'm worried about the next crop. That's why I'm in a hurry. If I can't harvest something, I'll be in serious trouble."
The floods are just the latest in a worsening series of climate-related disasters to hit the agriculture sector in Pakistan, where many farmers work small plots.
A shortage of homegrown wheat has forced the government to import 3 million tons earlier this year.
Chachar says the setback has him up against a wall.
"I pretend in front of the family that all is well, but in reality, things are very bad indeed."
In the province, authorities say the disaster wiped out more than 3,700,000 acres of agricultural land, and killed 435,000 head of livestock, creating a crisis that is forcing many families to go hungry.
"People are running short of food, leading to malnutrition among children," says Associate Professor Soomro at the Gulam Muhammad Mahar Medical Hospital.
Soomro worries that the worst is yet to come. "There are still people stranded by floodwaters but we have no idea how many," he says.
"This means that the number of sick people will only increase."
He adds an ominous warning.
"Next, we will face such things as hepatitis-A and typhoid."
