Highways, driveways, rooftops, parking lots and sidewalks cover about 12 percent of Rhode Island. Massachusetts and Connecticut are covered by a similar amount of cement, asphalt and shingles. These impervious surfaces rapidly funnel contaminated stormwater runoff into steams, ponds and rivers before the water has a chance to soak into the ground.

Flooding becomes both more frequent and more intense, and much of this polluted runoff ultimately ends up in three of southern New England’s signature resources: Narragansett Bay, Long Island Sound and Buzzards Bay. The many beaches, tourist attractions and fishing spots — both recreational and commercial — tied to the health of these waters are a significant part of the the region’s economy.

To better protect these vital waterbodies and other natural resources in southern New England, local environmental advocacy organizations have put the Environmental Protection Agency (EPA) on notice.

Earlier this month, Save the Sound, a bi-state program of the Connecticut Fund for the Environment, and Save The Bay, Rhode Island’s largest environmental nonprofit, submitted comments to the EPA regarding the federal agency’s Massachusetts General Permit for Discharge of Stormwater from Small Municipal Separate Storm Sewer Systems (MS4).

The water quality and ecological health of Long Island Sound and Narragansett Bay are heavily impacted by stormwater pollution from Massachusetts, according to both organizations. Nearly 70 percent of Long Island Sound’s freshwater inputs are delivered by rivers that flow through Massachusetts, and 60 percent of the lands that drain to Narragansett Bay are in Massachusetts.

Many of the tidal and coastal waters associated with these waterbodies are impaired by nitrogen and/or pathogens, according to the recently submitted comments. Impacts include low-oxygen dead zones, toxic algae blooms, damage to coastal marshes and bacterial pollution that closes beaches.

“From the far western end of Long Island Sound east to Narragansett Bay, twin scourges plague our region’s waters: bacterial pollution and nitrogen poisoning,” said Curt Johnson, executive director of Save the Sound. “Implementation of a strong municipal stormwater permit for Massachusetts will help keep our beaches and shellfish beds open, and return life-giving oxygen to our waters. The coastal waters where we swim, fish and boat provide huge environmental and economic benefits for our region, and we must join together to protect them. It’s time for EPA to get serious about stopping stormwater pollution into New England’s waters.”

The comments submitted by Save the Sound and Save The Bay ask that the EPA strengthen the permit by including:

Clear standards and implementation goals for green infrastructure retrofits of existing impervious surfaces.

A specified maximum time from the date of discovery, within which all illicit discharges and sanitary sewer overflows must be eliminated.

A more extensive and specific list of low-impact development measures that must be incorporated into local building codes to reduce stormwater runoff from new developments and redevelopment.

More robust public participation in the development of stormwater management plans, specifically an extended public comment period and opportunity for a public hearing.

“Stopping stormwater pollution upstream is a vital step to protecting downstream waters like Long Island Sound,” said Roger Reynolds, legal director of Save the Sound. “The sound’s water quality is at serious risk from stormwater runoff each time it rains, with pollutants like bacteria, nitrogen and phosphorous pouring off paved surfaces, through storm sewers, and ultimately into our bays and harbors. This pollution violates the federal Clean Water Act, and we need the leadership of EPA and the cooperation of every state in the sound’s watershed to solve it.”

In February, Save the Sound and seven other environmental organizations petitioned the EPA for a strengthened nitrogen reduction plan for Long Island Sound that includes Connecticut, Massachusetts, New York, New Hampshire and Vermont. The petition also demands that the agency use its existing authority to immediately slash nitrogen from urban stormwater, failing sewer pipes and antiquated septic systems.

Also in February, the Conservation Law Foundation (CLF) and the Charles River Watershed Association (CRWA) filed a notice of intent to sue the EPA for failing to uphold the Clean Water Act and for failing to require large, privately owned stormwater polluters to obtain permits for their polluted discharge.

The agency’s responsibility is clear: to ensure that waterways are safe for drinking, swimming and fishing, according to the notice. The EPA’s failure to require polluters to control their stormwater runoff puts the Charles River’s water quality at risk and places an unfair burden on municipalities and taxpayers to foot the bill for managing this pollution, according to both organizations.

Along the Charles River’s 80-mile course, from Hopkinton, Mass., to Boston Harbor, there are acres of strip malls, office parks and parking lots. In fact, according to the CLF, 80 percent of the land area in Greater Boston is paved.

“CRWA analysis has shown that pavement and parking lots are the number one source of phosphorus pollution in the Charles River,” said Robert Zimmerman, the organization’s executive director. “If we’re ever going to restore the river, stormwater runoff from these large paved areas must be addressed.”

When it rains and snow melts, water runs across impervious surfaces, picks up pollutants such as oil, antifreeze, dog waste and heavy metals. This toxic stew flows into every waterbody in the region and eventually makes its way to Narragansett Bay, Long Island Sound and Buzzards Bay.

Mashapaug Pond in Providence, for example, is so polluted that it’s long been closed to swimming and fishing. Stormwater pollution has caused algae growth in the pond, choking aquatic life and, because of highly toxic blue-green algae, and making it unfit for human contact, according to a CLF report.

Despite their known contribution to the pond’s pollution, none of the neighboring property owners is required to do anything about it, despite the fact that as much as 60 percent of the phosphorus pollution in the ponds at nearby Roger Williams Park, which is visited by close to a million people annually, comes from Mashapaug Pond, according to the 10-page report.

The Rhode Island Department of Environmental Management (DEM) says polluted stormwater runoff is widely recognized by scientists as the greatest threat to water quality. The agency has even documented how stormwater runoff from paved commercial and industrial properties is harming Mashapaug Pond and nine other ponds throughout the state.