PROVIDENCE — The health of southern New England’s coastal waters and its various, and vital, watersheds is improving, but major challenges remain, most notably stormwater runoff from urbanized areas.

In upper Narragansett Bay, for instance, raw sewage no longer floats at the surface, but hard-to-see contaminants, such as nitrogen and hydrocarbons, are impacting water quality. And no one knows how emerging contaminants such as perfluorooctanoic acid, triclosans, alkylphenols, PBDEs and pharmaceuticals are mixing with each other and the pollutants washed into urban waters by stormwater.

Janet Coit, director of the Rhode Island Department of Environmental Management (DEM), recently told ecoRI News that stormwater runoff is one of the greatest challenges when it comes to protecting the region’s waters.

“It’s going to require a lot of small actions,” she said. “We can’t deal with stormwater with just big tunnels.”

The Narragansett Bay Commission’s massive, and expensive, combined sewer overflow (CSO) project has made huge strides in reducing the amount of stormwater that ends up polluting Narragansett Bay. But it can’t and won’t solve the region’s runoff problems alone.

Neither will residential rain barrels, permeable pavers, parking-lot rain gardens and other so-called green infrastructure. Solving this complex problem will require education, collaboration, money, and commitment from state and local government, if the region wants to ensure that, in the near future, urban beaches are open, fish caught in these waters are safe to eat and maritime economies are protected.

Whether it’s Taunton, Worcester or Fall River, Mass., or Providence or Pawtucket, R.I., water quality is impacted by runoff that carries pollutants and harmful bacteria, closing most urban waters to swimming and fishing, at least for food.

Urban development has led to increased flooding, beach closures and limited access to waterways, with climate change serving to exacerbate these impacts, including those affecting marine life in Narragansett Bay, Buzzards Bay and Long Island Sound.

In many urban areas, however, site-specific efforts to address stormwater runoff are marking progress, according to the fifth annual Watershed Counts Report.

“The urban projects featured in this yearly report can and should help drive more, broader and integrated initiatives,” said Tom Borden, program director of the Narragansett Bay Estuary Program, which coordinates the annual report along with the Coastal Institute at the University of Rhode Island. “The benefits are not only environmental and societal, but have a direct link to enhancing the region’s economy.”

He noted that since the greatest pressures and impacts on the Narragansett Bay watershed come from its most populated areas, that is where the main challenges lie. The same holds true for Buzzards Bay and Long Island Sound.

“Our urban waters lack public access and continue to experience poor water quality conditions during much of the year,” said Jonathan Stone, executive director of Save The Bay. “Improving public access and reducing polluted runoff remain important priorities along the Providence and Seekonk rivers.”

Thanks to ongoing efforts — including those highlighted in the recently released Watershed Counts report — to improve urban water quality, the public beach at Sabin Point in East Providence could be safe for swimming in the next year or two, according to Borden.

“The Narragansett Bay Commission’s CSO tunnel has drastically reduced bacteria levels,” Borden said during a Nov. 2 Watershed Counts press event at Save The Bay. “Urban water quality is improving.”

Sabin Point is a popular destination, with picnic areas, basketball courts and playgrounds surrounded on three sides by water. But the fun currently stops at the water’s edge.

Since 2010, the Rhode Island Department of Health, in collaboration with Save The Bay and the city of East Providence, has monitored bacteria levels at Sabin Point and found that, with a little work, this could be the first licensed saltwater beach in Greater Providence, according to the 17-page report.

A licensed beach at Sabin Point would provide convenient recreational access to the tens of thousands of people, and has the potential to bring economic growth to East Providence with a parking sticker fee program, food stands, events and employment. The East Bay Bike Path provides convenient access.

While the waters off Sabin Point beach are improving, obstacles remain, such as relocating a stormwater outfall pipe. The pipe is at an angle that points back toward the beach, causing contaminated water and algae to back up in the area and attracting geese and other waterfowl. These birds then defecate in the water, which creates a breeding ground for pathogens that are harmful to human health.

Other cities also are adopting initiatives designed to protect urban water quality and improve public access. Pawtucket has renovated Festival Pier, a former waterfront brownfield. Worcester has planted tens of thousands of trees to help improve water quality. Taunton removed several dams to decrease downtown flooding and improve fish habitat, which also improves water quality.

“Partners are making investments that have important local impacts, but these isolated efforts need help to take on the big issues such as improving water quality and adapting to climate change,” said Nicole Rohr, assistant director of the Coastal Institute. “Unfortunately, the scale of effort that is needed is not currently in development.”

Development pressures, including population growth in urbanized areas, however, can’t be offset with new trees, underground tunnels and remediated brownfields.

Urban areas that abut natural resources, such as Narragansett Bay, directly and indirectly contribute to a higher level of pollution than is typically seen in more rural waters, according to the report.

The waterfronts of Providence and Fall River, for example, feature tanks storing fossil fuels, piles of coal, heavy machinery, scrap yards and miles of highway. Stormwater from these sources must be properly monitored and regulated, because runoff picks up pollution and washes it into local waters, making them unsafe for swimming, fish consumption and most everything else.

Urban areas are covered by vast amounts of impervious surfaces, such as roads, roofs and concrete, that don’t allow rainwater and snowmelt to seep into the ground and undergo a slow process of filtration. The fixes aren’t easy, but the rewards benefit the environment, public health and the economy.