All drainage systems have their limitations and New York City’s is 1.75 inches of rainfall per hour. Unfortunately for many New Yorkers, the storm that deluged the region on Friday dropped more than two inches between 8 a.m. and 9 a.m. — and then kept on coming.

The limit on the capacity of the city’s network of drains, pipes and water-treatment plants is the main reason New Yorkers across all five boroughs suffered through flooding. And this probably will not be the city’s last bout with heavy flooding as it plays catch-up with the pace of climate change, experts said.

“This changing weather pattern is the result of climate change, and the sad reality is our climate is changing faster than our infrastructure can respond,” said Rohit Aggarwala, commissioner of the New York City Department of Environmental Protection.

The rush-hour downpour on Friday overwhelmed the 7,400 miles of pipes that carry storm water and sewage under the city’s hard surfaces to treatment plants or into the nearest rivers and bays. The runoff backed up into the streets, causing flooding that swamped cars and seeped into basements and subway stations in Brooklyn and Queens.

The scenes of water rushing over roads and sidewalks were similar to those in 2021 when Hurricane Ida inundated the city and left 11 people dead in Queens. That storm was a warning sign, said Daniel A. Zarrilli, a special adviser to Columbia University on the institution’s climate and sustainability practices.

“We’re in this new territory where we’re seeing higher intensity rainfalls like this,” said Mr. Zarrilli, a former climate policy adviser to the mayor. “Once you’ve exceeded the capacity of the sewers themselves, that’s what causes these backups. When the pipes can’t handle it, it backs up.”

About 60 percent of New York City has a drainage system that combines storm runoff with sewage in the same pipes. When the flow through those pipes is more than double what the sewage treatment plants were designed to handle, the excess — a mix of rain and untreated sewage — goes straight into local waterways like the Gowanus Canal in Brooklyn, the East River or Jamaica Bay.

But as the sewer system backs up, some of that untreated wastewater winds up in the basements of homes and businesses around the city, said Dave Balkan, who runs Balkan Sewer & Water Main Service in the Richmond Hill section of Queens.

“When it gets inundated to this degree, it backflows,” Mr. Balkan said. “That’s when regular people start having sewer water bursting out of their drains or their basement toilets.”

His company was “getting tons of calls” from distressed and disgusted homeowners on Friday. He said he responded as a courtesy, but “at the time it’s happening, there’s nothing you can do for them.”

They just have to wait for the system to clear and pull the muck back through the pipes, Mr. Balkan said. He was reluctant to estimate how long that would take because the storm had lasted so long.

“Usually we get a flash storm, but it’s kind of been raining all week,” he said. “This is an event.”

Solving the city’s growing problems with storm water will require “a lot of investment in infrastructure and a lot of creativity,” Mr. Zarrilli said.

A 2021 report from the city called “The New Normal” estimated that “recalibrating our sewers for storms like Ida” would take decades and cost $100 billion. Upgrading the system in Southeast Queens alone cost $2 billion, it noted.

In the meantime, the city has been working with federal officials to create some places for the excess water to go, other than straight into the sewer system, and potentially into the waterways, said Ben Furnas, a former director of the Mayor’s Office of Climate and Sustainability who is now executive director of the 2030 Project at Cornell University.

“There are lots of strategies to make a place for the water to go and be stored so it doesn’t end up tipping off into the creeks or canals,” Mr. Furnas said. He said significant investments had been made in “gray infrastructure” like large holding tanks and “green infrastructure” like gardens set in sidewalks that can absorb some of the rainwater.

“It’s a really challenging problem to solve because we have this legacy infrastructure system and its capacity is being exceeded,” said Franco Montalto, a flooding expert and engineer. “You can either manage excess water underground or you manage it on the surface.”

Dr. Montalto cited an initiative in Copenhagen, where officials redesigned streets to hold water temporarily. Certain intersections, he explained, are depressed or sunken, to draw water away from neighborhoods and allow it to pool at a depth that is safe for cars to pass through. Eventually, the water runs off into parks and other green spaces.

Upmanu Lall, an engineer and the director of the Columbia Water Center, said he would like to see more pumps installed in the city’s sewer system to move excess water and prevent overflows. “We have limited capacity to discharge the water, which leads to more possibility for internal flooding,” he said.

Candace Agonafir, who conducts research with Dr. Lall, said one factor in the disastrous flooding during Hurricane Ida was the accumulation of trash and other debris that blocked the rain from getting into the sewers.

Dr. Agonafir was part of a study that looked at flooding in the city through 311 complaints. It found that “for an appreciable number of ZIP codes, infrastructural complaints were found to be predictors of street flooding complaints.”

And one way to address it, the study noted, involved “improving the internal and external components of the drainage network” to “reduce some of the physical and economic impacts of street flooding in metropolitan areas.”