The problem is as old as asphalt and as hard to fix as tapping a tight town budget.
There is so much pavement that when it rains, water that in years past would have soaked into the ground now shoots off downhill toward the nearest stream.
The Wissahickon Creek is emblematic of the problem: Its first trickles emanate from the Montgomery Mall parking lot.
In the last decade, engineers, regulators, and developers have embraced the idea of turning parking lots, fields, and roofs into giant sponges that hold rainwater long enough to let it percolate into the ground.
Philadelphia has been touted as being emblematic of the solution: Its $2 billion plan to foster a plethora of smaller swales, gardens, green roofs, and more - instead of a giant underground tank that simply holds the water until it can be treated - is considered a national model. The city already has 10 acres of green roofs. But the whole plan is going to take 25 years to implement.
Part of the region's problem stems from the fact that so much of it was built before regulations for storm water existed.
"In the storm-water world, the 1980s was the beginning of the first shot at storm-water management," said Chad Pindar, supervisor of watershed planning and compliance for the Delaware River Basin Commission, an interstate agency. "Anything built prior to the '80s, you can write off."
Gradually, as the problems became harder to ignore, new techniques emerged and regulators responded.
"By the early 2000s, you started to see better management," Pindar said.
But it was aimed mostly at new construction. "The big hurdle is what do you do with Darby Borough? It's already built out," Pindar said.
Only recently have officials begun to enact regulations applying to redevelopment. So improvement is going to take a long time.
Gradually, smaller changes have come.
After devastating floods along the Delaware in 2006, New Jersey developed new rules to preserve the vegetation along streams - the riparian buffer - to reduce erosion and aid absorption.
Before, setbacks of 25 and 50 feet were required; now, they must be 50, 150 and 350 feet. "That storm heightened our recognition that these areas are prone to flooding, and that the current rules didn't do enough," said spokesman Larry Hajna of the New Jersey Department of Environmental Protection.
Decades ago, the state of the art was detention basins, which were basically large ponds designed to hold water during a storm and release it slowly afterward.
But Temple scientists have looked at about 600 such basins in the Pennypack and Wissahickon watersheds, and many no longer work. They have become silted in, or the drains are blocked by trash. Some were poorly designed and never really worked at all.
In 2003, Pennsylvania began to require new development to install measures that promote absorption, said James Newbold, manager of the Department of Environmental Protection's watershed-management program.
Villanova University's campus is a lab for the newest methods, overseen by Rob Traver, director of the Center for Sustainable Engineering.
Some buildings have roofs topped with gardens. The campus also has 13 rain gardens - sites using plants and a sandy soil to help water soak back in.
During Irene, "all of our sites did very well," Traver said. "But once the rainfall gets over four or five inches, how much good does it do? Probably not a lot."
Some of the region's newest buildings have rain-catching systems, reflecting that rainwater can be a resource. They use the water to flush toilets.
But now, officials are wondering how to factor in climate change. The predictions call for more rain - and more floods - in the future.
Climate data from New Jersey shows rainfall amounts rising. Precipitation data from the Philadelphia Airport shows that four of the Top 10 storm events in the last 65 years came in the last five years.
Add everything together and "all these changes are making it more complicated for developers, for water planners," and others, said Temple's Featherstone. "If I were the master of the universe, I would put a cushion on floodplain regulations," requiring wider setbacks to allow for changes.
Where is progress being made? Featherstone points to Upper Dublin, where Township Manager Paul Leonard said the Fort Washington Office Park has become "the poster child for flooding" because it is inundated so often.
Some of the flooding is due to bad land-use decisions decades ago. Some of it is due to upstream development. Either way, "we've had some real doozies," Leonard said.
Now, the township is instituting zoning changes to steer development uphill.
Months ago, engineers completed a plan for two "dry ponds" - basically acting like dams during storms - to address much of the flooding.
But it is an expensive undertaking. Engineering costs alone were $1.3 million. Building the project will cost $16 million to $18 million, roughly equal to Upper Dublin's annual budget. They need help with funding.
Meanwhile, did the industrial park flood during Irene? Absolutely.
For Carol R. Collier, the basin commission's executive director, the bottom line is that "things are changing. We need to be more adaptive."
She learned a saying long ago: Mother Nature always bats last. "I always keep that in the back of my mind."
Contact staff writer Sandy Bauers at 215-854-5147, firstname.lastname@example.org, or @sbauers on Twitter. Visit her blog at philly.com/greenspace