A settlement reached in federal court promises an accelerated attack on pollution from the labyrinth of pipes under Boston and from pavement runoff, an effort designed to prevent raw sewage and other pollutants from reaching area waterways.
Pollution has remained an episodic problem — despite the $5.5 billion Boston Harbor cleanup — prompting beach closings and deterring those ready to dip their toes into the water. It is also a significant problem in fresh water, such as the Charles River, where storm runoff this year is contributing to blue-green algae blooms that can be a health risk to humans and animals.
The agreement, reached last week, comes two years after the Conservation Law Foundation and the US Environmental Protection Agency sued the Boston Water and Sewer Commission for not acting quickly enough to stop the pollution, largely from storm drains and illegal sewer pipe hookups.
“Boston is entering a bold new phase as a city poised to lead the nation in clean water,’’ said Anthony Iarrapino, lead attorney on the case for the Conservation Law Foundation.
The agreement includes a penalty of $395,000, but the real cost will be much higher as the Water and Sewer Commission fixes problems that it promised to correct under the agreement. John P. Sullivan Jr., chief engineer of the water agency, said ratepayers will see increases as a result of the settlement, but he said the agency will not know how much until it performs an analysis next year.
“We were doing many of these projects anyway,’’ said Sullivan, whose assessment was echoed by local environmental groups and the Conservation Law Foundation. “Now, we have strict deadlines.”
While Boston is considered among the nation’s most progressive communities in dealing with sewage as part of the Boston Harbor cleanup, the remaining problems have become the most challenging to fix because pollution is not coming from one obvious source anymore. Last August, a deluge carrying pollution overwhelmed storm drains and triggered the closing of more than 2 miles of beaches, from Pleasure Bay to Carson Beach.
One major problem is asphalt and concrete: The impermeable surfaces do not allow rainwater filled with pollution from city streets and sidewalks to seep into soil, which would allow toxins to naturally filter out. Instead, the pollution travels on a storm drain highway, reaching Boston Harbor and other waterways.
To help figure out solutions, last week’s settlement requires green makeovers at City Hall Plaza, East Boston’s Central Square, and Audubon Circle in the Fenway-Kenmore neighborhood. The three urban landscapes will undergo a redesign as quickly as possible. That means residents and visitors could soon see tree boxes or rain gardens that hold water and filter out pollutants in those locations, among other items being discussed. Environmental groups hope those demonstration projects start a green redesign revolution across Boston.
“Green infrastructure can improve the look and feel of the urban landscape,’’ Iarrapino said.
The second major component of the plan is an attack on illegal sewer hookups. In the 1940s and ’50s, Sullivan said, residents and businesses may have inadvertently or intentionally hooked up toilets or washing machines to storm drains instead of sewer pipes. Back then, with raw sewage being dumped into Boston Harbor, distinguishing between the pipes probably did not mean as much as it does today.
But as Boston Harbor has become progressively cleaner, and sewer and storm drain lines are separated, the illegal hookups have emerged as a bigger pollution problem.
Boston Water and Sewer has already repaired 1,236 illegal hookups since 1985, preventing 630,770 gallons of raw sewage a day from draining into waterways, Sullivan said. To trace illegal hookups, sewer workers painstakingly place sandbags down storm drain manholes. They return a few days later — as long as it hasn’t rained — to see whether sewage or evidence of detergents from washing machines is trapped behind the sandbags. They then move to the next manhole to determine whether it is closer to the source and repeat the exercise.
After they identify a house or group of homes that may be contributing to the pollution, they ask to put dye in owners’ toilets or washing machines to see if the dye then shows up in the storm drain.
“It is very, very labor intensive . . . but it doesn’t even matter the volume,’’ said Sullivan said. “Imagine one flush on the beach where your kids play.”
The settlement also requires a host of new or more aggressive timetables for other monitoring, computer modeling, and the identification of sewer pipes that can clog and back up onto city streets or into homes.
Kate Bowditch, director of projects for the Charles River Watershed Association, was most pleased about the settlement’s requirement that city departments work together to redesign the urban landscape.
“This is huge,’’ she said. “It should mark the beginning of a real shift in the way the city has been handling stormwater.Beth Daley can be reached at email@example.com. Follow her @Globebethdaley.