The Environmental Protection Agency announced new draft requirements on Thursday that could compel about 4,000 commercial properties across Massachusetts to take steps to limit stormwater runoff that’s polluting the Charles, Mystic and Neponset rivers.

The rules target large private properties like malls and universities that are within the rivers’ watersheds and that have more than an acre of impervious surfaces, including roofs and parking lots. The draft EPA permit would require those property owners to take steps to reduce stormwater runoff, like creating rain gardens or underground systems.

Already, the draft rules are being celebrated by environmental groups, but some say the proposed pace of their rollout is far too slow. At the same time, a group representing property owners says the requirements would pose a excessive financial burden.

The proposed requirements don’t go into effect immediately. They now enter a comment period, and public hearings on the topic will be held in January.

“The ultimate goal is to meet water quality standards in all three rivers. And those are set by EPA,” Damien Houlihan of the EPA said Thursday on a call with reporters. “And currently all three rivers are what we refer to as 'impaired’ for both nutrients — which includes things like phosphorus — and bacteria. So we want to ensure that the goal of the Clean Water Act of fishable, swimmable waterways is met. And that’s what this action is designed to do.”

Houlihan said the proposal as written would affect nearly 2,300 commercial, industrial and institutional properties in the Charles River watershed. Nearly 1,000 properties in the Mystic River watershed and over 800 in the Neponset River watershed would be included.

Julie Wood of the Charles River Watershed Association said the requirements would help with water quality.

“Right now, most of that stormwater pollution is not treated. It just goes straight into our streams and rivers and causes significant damage,” Wood said. “Stormwater pollution is the number one source of pollution to the Charles River.”

The requirements wouldn’t just apply to properties that touch the rivers. Stormwater from properties around the watershed is sent to rivers through underground pipes, she explained.

“What that has also meant up until the issuance of this new permit is that the city or town then became responsible for the pollution,” Wood said. “So even though the pollution was being generated on private property, these private properties were just allowed to essentially dump it into the city or town’s system and have it be the city or town’s problem. So now with this new permit, the properties that are actually generating the permit are going to be responsible for cleaning it up.”

But Wood said the EPA’s proposal gives commercial property owners too long to comply.

“It’s over ten years for these on-the-ground changes to happen,” she said. “So when you’re talking about actually seeing improvements in the river, it’s a pretty long timeline, especially given the current impacts to the river that stormwater runoff is causing.”

Houlihan said the EPA understands those concerns.

“This is a draft permit, so we’re expecting we’ll hear a lot of from folks about that timeline and we will be able to adjust accordingly to what we heard,” he said. “We think what we’ve put forward is a reasonable timeline. Taking into account these are a whole entirely new universe of permittees that have never been regulated before, that the industry itself needs time to develop and gear up to make some of these improvements, and that it would be a phased approach over many years for tackling the biggest properties first and then the smaller properties later. So that’s our reasoning for establishing the timelines.”

Tamara Small, the CEO of the commercial real estate development association NAIOP Massachusetts, said that back in 2010, the estimated cost for property owners in just the Charles River watershed to comply with a similar proposal was $1 billion. These new requirements would cover two additional watersheds.

“So many, many more communities and certainly many more property owners,” she said. “Furthermore, it also applies to mixed-use properties. So that means you’re going to be potentially pulling in housing units.”

That could add a burden that would slow residential development in the midst of a statewide housing crisis, Small said. Office buildings would also fall within the permit at a time when vacancies are high, she added.

“The value of those properties far, far less than when they were purchased even just a few years ago,” Small said. “So now you’re adding on some extraordinarily high operating costs to these owners. They will not be able to make that work. So if this is a priority for the federal government, then the federal government must be stepping forward with subsidies to make this work. Otherwise, I don’t see a way forward for many of these properties. They will not be able to comply with the program.”

Small said her organization plans to submit detailed technical comments to the EPA during the comment period.

“I think what’s really important is we need to find ways that protect the environment but also are fair and equitable and not cost prohibitive,” she said.