Milly Vega knew the water inundating her quiet side street near the Saugus River in Lynn, Massachusetts, last September was trouble. She wasn't ready for what came in her basement at the same time.
"The water was darker than usual," she said in an interview. "And it wasn't clear, Mother Nature water. It was coming through the sink, through the toilet."
Water gushed out of the toilet in her finished basement, rising several feet high and destroying her furniture and mementos.
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"It wasn't normal and unfortunately, we had to break the wall three feet. They had to cut through the walls three feet," she said. "I had four days of the fans, the humidifiers, and everything was commercial."
The damage cost tens of thousands of dollars, she said. And contractors still are working on her basement.
Lynn is no stranger to flooding, and climate change is expected to make the problem more devastating to more people.
But, experts and residents said, Lynn's century-plus-old sewer infrastructure, in desperate need of replacing, may be contributing raw sewage backups into homes and streets, and making the inevitable flooding even worse.
A monthslong NBC10 Boston investigation revealed major sewer projects that could have mitigated flooding and ended sewage backups were crippled by poor planning, questionable oversight, and legal wrangling, leaving Lynn residents who have been dealing with floods and sewage for decades in the lurch.
Officials at the Lynn Water and Sewer Commission, the agency independent of the city government that operates and maintains the sewer and storm systems, pointed fingers at its former contractor, and state and federal environmental regulators.
"We were told by the federal government and the DEP 13 years ago to stop and submit another plan. We submitted another plan to the DEP and the EPA and they sat on it for so many years," Bob Fennell, the commission's deputy director, told NBC10 Boston in an interview.
The EPA, in a statement with DEP, pushed back on the accusation.
"EPA strongly disagrees with the statement from the deputy director provided to NBC10," the EPA said in its statement.
It added that it believes a new court-ordered plan Lynn is working on puts the city "on a path towards addressing the sewer overflow issues that have adversely affected the citizens of Lynn all these years."
Vega, her neighbors, and thousands of others in neighborhoods west of Commercial Street to the Saugus River have been complaining about sewage backups for years, according to state documents and videos of public meetings.
But already, Lynn seems in danger of dropping the ball, failing to do a key set of tests related to the design of the new project and submitting several plans state and federal officials criticized as lacking specifics. DEP also warned the commission that it is understaffed, and its maintenance program is reactive.
Lynn Water and Sewer officials said the department is doing everything it can to reduce flooding and sewage backups, and maintain that it has been proactive in working with state and federal environmental regulators.
"We've signed a timeline with the federal and state governments, so it has to be done," Fennell said.
Old cities like Lynn have outdated sewer systems that carry both storm water from the gutters and waste water from homes and businesses in a single pipe to the municipal treatment plant.
During heavy rains, the volume of the water and sewage combined can be greater than the system can handle. In that situation, the system discharges everything—rain and raw sewage — into a body of water through dedicated overflow pipes. In Lynn, those discharges went into the Saugus River at Summer Street, Lynn Harbor off the Lynnway, and at Kings Beach next to the Swampscott border.
But even that isn't always enough, and if it doesn't go out, it has to come back up. The combination of the storm water and sewer systems means that backups caused by rain in the storm drains have a direct line into the streets, and into homes.
Annalisa Onnis-Hayden, a civil engineering professor at Northeastern University, said separating those systems can lessen flooding because the single dedicated storm system have more capacity to carry away rain water. It also would end sewer backups into homes and streets.
"If it's separated, the rain wouldn't affect the amount of sewage," she said. "Only the storm drain will be affected by the storm water."
The EPA first sued Lynn in 1976 for discharging sewage into the Saugus River, Lynn Harbor, and Nahant Bay, a violation of the Clean Water Act.
After changes is federal law, the EPA in the late 1980s finalized regulations designed to end the discharge of raw sewage from combined systems.
A number of cities around the country, including Lynn and Boston, entered into court-enforced consent decree agreements with the EPA to end those discharges.
Through the 1990s, Lynn made progress separating the storm water and sewer lines in part of the city along the Saugus River north of Boston Road, and other work.
That progress led Lynn to renegotiate its agreement with the feds to update goals and create a new timeline.
In 2000, Lynn and its contractor, USFilter Operating Services Co., submitted a plan to separate three large sections in the eastern part of the city, including parts of downtown and the area along the Swampscott border north past Peabody to Lynnfield.
That plan formed the basis of a second consent decree, approved in 2001. Work began in the easternmost sections of the city.
But the plan was plagued with problems. Emails and DEP documents from 2002 and 2003 show that engineers and regulators grew increasingly concerned that Lynn's measurements badly underestimated different water flows.
"How did the commission get itself in this mess?" one engineer asked in a 2003 email.
After complaints to DEP about sewage backups in West Lynn, DEP in 2003 ordered the water and sewer commission to reevaluate its entire plan, and its system, to account for concerns about water flows and to determine what it would take to end the sewage backups in West Lynn.
A new contractor, Camp, Dresser, & McKee (CDM), conducted the evaluation and noted that large neighborhoods in the western part of the city also had combined sewer and storm systems. But those areas, and all the water flows from them, were completely left out of the 2000 plan.
DEP seemed surprised by this information.
"The omission of the Bennett Street and Shepard Street areas in the October 2000 facilities plan update undermines the (combined sewer overflow) performance of the present plan and creates the potential for sewer backups and street flooding," DEP wrote in a December 2003 DEP response to the Camp, Dresser, & McKee report.
All that water and sewer from those neighborhoods were unaccounted for, and would actually cause more problems if the 2000 plan were to be completed, the report concluded.
"The CDM report indicated that at the completion of the East Lynn sewer separation work in the (eastern) areas, as presently designed ... system-wide flooding and sewer backups will increase when compared to current conditions," DEP said in its response.
Because the plan would fail, DEP, ordered much of the separation work to halt.
In October 2004, Lynn, working with CDM, filed a new separation proposal that included the western neighborhoods left out of the 2000 plan.
The EPA and DEP did not approve or respond to that proposal. By 2005, Lynn was embroiled in a yearslong lawsuit with USFilter over the contract to design and implement the 2000 plan.
That lawsuit took five years to resolve. Some work continued, and the separation work in the section of the city along the Swampscott and Peabody lines was completed.
But no other work was started.
Dan O'Neill, director of the Lynn Water and Sewer Commission since 2004, would not agree to numerous requests for an interview with NBC10 Boston.
He also would not answer a list of specific questions emailed to him asking who at Lynn Water and Sewer approved the failed 2000 plan, why West Lynn was left off, and what role O'Neill, who was the commission's chief engineer at the time, played in molding, informing, and overseeing the plan.
Fennell, who came out of the water and sewer commission's office for an interview when NBC10 Boston Investigators arrived asking to see O'Neill, said the commission is doing everything it can to help residents and abide by the consent decree.
"We're trying to get them the relief by separating the storm water and sewer water," Fennell said. "We're working towards that goal."
But the commission has already asked DEP for a one-year extension on its planning after failing to complete a set of groundwater tests last spring.
It also does not clear storm drain basins, which over the entire system can hold a lot of water, annually, as the commission said was the standard.
According to water and sewer commission work records obtained by NBC10 Boston, most drains in the city, including in flood prone areas, have only been cleared once in either 2016 or 2017.
DEP told the commission in a May 26, 2017, letter to the commission that it is understaffed, and that its maintenance program is a "'reactive' program with little preventative maintenance," and recommended a "preventative maintenance program."
It also warned the commission in a separate letter on May 26, 2017, that the extension on the groundwater testing "cannot affect the commission's responsibilities for moving forward with the CSO abatement work required under the Third Modified Consent Decree."
Meanwhile, residents like Milly Vega and her neighbor, Sherry Pacewicz, flinch at the first forecast of rain.
"I'm worried that we're going to have another flood, and we're not even done cleaning up this one to clean up another one," Vega said. "Everything that we've bought to get it repaired, we could lose it again tomorrow."
Editor's note: This story has been updated to reflect the correct spelling of Onnis-Hayden's name. We apologize for the error.