Called "Green City, Clean Waters" and proposed in 2009, the plan "is our pledge and our investment to make our rivers and streams fishable, swimmable, and breathtaking," said Howard Neukrug, the city water commissioner.
The agreement "signals our recognition that the best way to manage storm-water runoff is to control it at its source," said Jenifer Fields, head of the DEP's regional water-quality program.
Although the plan remains controversial among some business owners for its fees, it has the mayor's support.
Officials contend the plan - because of all the trees and plants - will help beautify the city, revitalize neighborhoods, clean the air, cool the region, and save energy.
They also say the plan is cheaper and better than the route some cities have taken - building miles-long underground tunnels that act as giant reservoirs for storm water until it can be gradually pumped out and treated at a sewer plant.
"It's extremely innovative," said Robert Traver, a Villanova University professor of civil engineering and a national storm-water expert. "Other places are watching this, and they're going to be following our lead."
Some projects are already in place. Far more are coming.
The problem the plan attempts to solve is called "combined sewer overflows."
While some cities have separate systems - one for regular sewage, another for storm water - most of Philadelphia has a combined system, sending all water waste into one matrix of pipelines.
This works when the weather is dry. But when it rains, the system becomes overwhelmed, and storm water that is now carrying raw sewage and other contaminants gushes into streams.
One group that has opposed the plan from the outset is the Unified Building Owners of Philadelphia, which represents 100 of the largest businesses in Philadelphia, according to its chair, Stuart Parmet.
It was formed specifically to fight one part of the plan - a new way to charge for storm-water treatment.
Previously, businesses were charged based on the water they used, on the notion that what goes into a building eventually comes out. Now, however, fees are based on a recognition that properties produce storm water when it rains, and the city bears the expense for treating it.
The problem is that businesses with little water use, but with large roofs and parking lots that rainwater sluices from, face steep hikes.
Parmet, owner of American Box & Recycling Co., said his monthly fees would increase from $300 to $4,900. In a tight economy and with many jobs going to the suburbs, this is a fee Philadelphia businesses can ill afford, he said.
The Water Department has agreed to cap the increases at 10 percent a year for the next two years, but Parmet said the plan was still "ineffective and inappropriate."
Businesses can avoid the fee by putting in gardens or porous pavement to reduce runoff. But Parmet said it would cost his company $350,000 to meet the specs.
"To renovate something or make it green would have been great if they gave us eight or nine years to plan," he said. "So people wouldn't have spent hundreds of thousands of dollars to blacktop areas or put new roofs on."
Others praised the new fee structure as equitable.
Overall, "this is the kind of technology we wish more cities were using to manage storm water," said Brady Russell, eastern Pennsylvania director of Clean Water Action. "High fives all around."
But he is worried about the maintenance that many projects will need. Porous streets have to be vacuumed so debris doesn't clog the pores. Rain gardens have to be weeded.
"This is going to be throughout the city, on land owned by multiple agencies," Russell said. "The Water Department is going to have to keep an eye on it all."
Lawrence Levine, senior water attorney at the Natural Resources Defense Council, a New York-based nonprofit advocacy group, called the plan "a national model for how to clean up polluted urban waterways."
Levine said it's the first plan he knows of in which a city will get credit for managing storm water when private property owners install green infrastructure.
The city now requires large developments or redevelopments to install systems to capture runoff.
The Water Department is developing plans for homes, schools, public facilities, parking lots, industry, and others, offering technical assistance, design services, and incentives for green storm-water projects.
Although the plan was formally approved Wednesday, the city has been incorporating and recognizing projects for more than a year.
Columbus Square in South Philadelphia has huge planters that detour rainwater. Nearby at Second and Reed, a playground incorporates garden areas to hold runoff.
On Earth Day, U.S. Environmental Protection Agency administrator Lisa P. Jackson came to town for a tree-planting in a rain garden at Kensington High School for the Creative and Performing Arts - one part of a "Big Green Block Initiative" that is a prime example of what could happen throughout the city, Neukrug said.
Not long after, Mayor Nutter dedicated the city's first street with porous pavement - the 800 block of Percy Street in Bella Vista - by pelting the pavement with water balloons and watching the liquid disappear.
Percy was chosen because the street needed other repairs, a tactic officials plan to repeat. Repaving streets just for the sake of going green would cost too much.
Eventually, says the Water Department's deputy commissioner of environmental services, Chris Crockett, projects that are actually visible - like the planters - "are going to be as commonplace as manhole lids."
Contact staff writer Sandy Bauers at 215-854-5147 or email@example.com.
Visit her blog at http://go.philly.com/greenspace.
For more on the plan, see http://www.phillywatersheds.org/