New regulations from the Environmental Protection Agency will take steps to reduce stormwater runoff, a major source of pollution in the rivers and watersheds in the Boston area.

Reduction by cities and towns of that runoff — when falling rain and melting snow can pick pollutants on roofs and roadways and carry them into nearby freshwater bodies — has been regulated for decades, but to date private property owners haven’t held responsibility for mitigating that pollution.

The new permit, the draft of which was released for public review Oct. 31, would bring the owners of those properties into the effort to reduce runoff.

“These stormwater discharges have been unregulated for decades and decades,” said Heather Govern, vice president of clean air and water at the Conservation Law Foundation. “We’ve been wanting to see a permit like this that actually regulates this pollution for a long time.”

The permit will create guidelines around how private commercial, industrial and institutional landowners with one acre, or more, of impervious surfaces — think non-green spaces like asphalt, roofs and paved parking lots — within any of the three watersheds must mitigate stormwater runoff from their property. Within the Neponset River’s watershed that would be about 800 properties, with another 3,300 in the other two watersheds.

Its release follows action from the Conservation Law Foundation and the Charles River Watershed Association, which petitioned for — and ultimately filed a lawsuit against the EPA regarding — a lack of regulation for private property owners in the watersheds. The groups are celebrating the release of the draft permit but have concerns about the current timeline proposed for its implementation.

The draft regulations are especially focused on phosphorus, which can enter waterways when things like fertilizer are caught up in rain flowing over those impervious surfaces and are swept into waterways.

Increased levels of phosphorus in waterways can lead to impacts like cyanobacteria blooms — rapid increases of blue-green algae populations in rivers and other bodies of water — which can release toxins into the water, which can be harmful to humans and animals.

On Nov. 8, the Boston Public Health Commission released a health advisory due to a cyanobacteria bloom in Sprague Pond in Hyde Park, which falls in the Neponset River watershed. For two weeks in September into October, a separate advisory was declared for a section of the Charles River alongside downtown Boston.

In each of the watersheds, the permit will create a goal to reduce phosphorus levels in the river about 60% — the exact number varies by river.

And the same efforts that property owners would likely take to address phosphorus reductions would have other benefits too, like limiting the amount of bacteria from animal waste that gets washed into rivers, or reducing the amount of road salt in the winter, which can impact wildlife as the salinity of the freshwater rises.

“Some people think that water goes to a water treatment plant like water from sewers do, but it doesn’t,” said Anna Yie, the green infrastructure specialist at the Neponset River Watershed Association. “It usually goes directly into a local water body.”

Water that flows down a storm drain in front of a home or office is likely pumped to the nearest stream or pond without any processing.

Creating guidelines for private property owners addresses what is currently a gap in efforts to address runoff pollution, Govern said.

Under existing regulations, for decades, cities and towns are required to get permits that require mitigation of stormwater runoff pollution. Without any restrictions or for private property owners, the onus of addressing the issue has fallen only on municipalities, even as many of the impervious surfaces in the watershed are privately owned.

“The regulators and the public have always recognized that municipalities should be responsible for reducing the pollution in their cities and towns,” Govern said. “Now we have the missing link, which is to require that private property owners also take responsibility for the amount of pollution that they are discharging into these nearby rivers.”

For municipalities along the Neponset River, the new permit is a welcome change, said Ian Cooke, executive director of the Neponset River Watershed Association. Under existing regulations, the municipalities are currently entirely responsible for addressing stormwater runoff, even as much of the land — within the Neponset watershed about two-thirds of it, according to Cooke — is privately owned.

“It leaves municipalities trying to solve the whole problem while having direct control over less than one-third of the land,” Cooke said in an email.

By addressing those privately-owned impervious surfaces, the new requirements should make reduction of runoff simpler and more cost-effective, he said.

And both the causes and impacts are ultimately regional. Though municipalities (under the existing permits) and private property owners under the new draft permit will have their individual reduction responsibilities, how the pollution impacts play out move across the watershed.

“This is a problem that crosses all sorts of boundaries,” Yie said. “Water doesn’t follow property lines and water doesn’t follow town lines.”

How stormwater pollution will be mitigated can take a number of forms. Yie said those approaches are often split into two groups, referred to as structural and non-structural controls.

Structural controls take the form of adding new infrastructure — things like adjusting the setup of storm drains or adding in green infrastructure like rain gardens that catch the runoff and let the water filter back into the watershed without the pollutants.

Non-structural controls are changes to how property owners handle the impervious surfaces they own. Those could include how and how often storm drains and catch basins are cleaned as well as running street sweeping regularly.

But Yie said she expects the change to be a shift in mindset as much as in practice. While many of the specific controls for addressing runoff might be relatively simple, the administrative work of applying for the permit and developing a plan to address stormwater will be new to many of the private property owners who will be required to take steps under the new permit.

“This is going to be maybe a new way of thinking about sites and operations and maintenance and upkeep in a way some people haven’t had to think about before,” Yie said.

But, while the permit is expected to bring benefits to watersheds, the timeline for the rollout of the permit remains a point of contention for advocacy groups.

Under the current draft, property owners would then have 11 years to fully reduce the runoff pollution from their land — an interim 6-year deadline would require a 50% reduction of the pollutants.

Govern said that she doesn’t expect those extended deadlines to bring in early action. In the experience of the Conservation Law Foundation, she said, under long deadlines like these, property owners and municipalities tend not to take action until about a year before the deadline comes into effect.

For control measures that are relatively simple, she said that she would rather see a five-year timeline for the full reduction — deadlines that she thinks are still generous.

“These are really simple measures that are required in the permit — literally, ‘reduce the amount of salt you use to de-ice your parking lot,’ ‘conduct more sweeping of your parking lot,’ ‘pick up trash,’” she said. “These are not difficult requirements for property owners.”

And those 11-year timelines only go into effect after the permit is officially authorized, which will likely, at the earliest, be in the spring following the EPA’s 90-day public comment period, which runs through Jan. 29.

The authorization timeline could also be slowed if industry groups mount legal challenges against it, something Govern said the Conservation Law Foundation is anticipating.

“I would say that we will not see any significant water quality improvements in these water bodies for at least 15 years due to the extended timelines and deadlines that have been written into this draft permit,” Govern said.

The extended timeline is also of concern for groups like the Neponset River Watershed Association.

“While we generally think it’s great that the EPA is moving forward, we hope to see EPA start requiring more action sooner than the 11 years from now called for in the draft,” Cooke said.

One glimmer of hope for speeding up the process: That timeline isn’t set in stone until the public comment period is over and the final permit is released.

Govern said pushing for changes in that timeline throughout the comment period will be a priority for the Conservation Law Foundation.

The EPA is also specifically seeking feedback on a handful of other pieces of the permit’s regulations, like if and how multifamily residential properties should be governed by the requirements, how owners of multiple properties next to and separate from each other should be regulated and what the impact of the permit might be on historic properties in the three watersheds.

While pieces of the whole puzzle remain in doubt as that process gears up, Yie said the region has the benefit of having seen municipalities learn to adjust to regulations like these.

Kicker: “The good news is towns and cities have figured out how to do this,” Yie said.