On sunny days, you might have to look a little harder to find evidence of sewage overflows on the Jones Falls Trail. But it’s there.

While walking along the path popular among runners and bikers, David Flores, the harbor waterkeeper with the advocacy group Blue Water Baltimore, pointed out toilet paper, female sanitary pads and flushable wipes that escaped the sewer system during a recent rainstorm.

He said when it rains especially hard, the lids pop off manholes in the streets.

"A tremendous amount of sewage comes up. It floods out the roadway. It floods out the trail," he said. "Most of it ends up going right back down into the river, but then you have ponding and then obviously you have debris that remains."

Baltimore officials estimate that more than 282,000 gallons of sewage and rainwater have spilled into the Jones Falls stream since the beginning of September.

And Jones Falls isn’t the only problem area. Also this month, another 58,000 gallons of sewage has poured into the Inner Harbor. When flash floods ravaged Elliott City and parts of Baltimore at the end of July, city officials estimated that more than five million gallons of combined sewage and rainwater contaminated the Gwynns Falls stream.

"We’ve seen people, not just here but elsewhere — on the east side, in West Baltimore — walking through, driving through sewage during storms, probably thinking it was just storm water, ponded storm water, when it fact it’s sewage coming up out of sewer lines under the street," Flores said.

The city has been working on repairs to stop the overflows for nearly 15 years. In 2002, federal regulators said the leaky sewer system violates the Clean Water Act, and the city entered into a consent decree with the Environmental Protection Agency and the state Department of the Environment.

The agreement required the leaks to be fixed by January of this year. Once it became clear that the city would miss the deadline, officials began negotiations over an extension that would push the deadline to the end of 2030.

In total, the city expects the repairs to cost more than $2.1 billion, most of which comes out of residents’ water bills.

Baltimore officials are quick to point out that overflowing into streams and rivers is how the sewer system was originally designed to work.

Pipes are never completely waterproof, said Dana Cooper, the chief of legal and regulatory affairs at the city Department of Public Works. Rainwater will always find a way in.

"Eighty, 90 years ago, it seemed like a good idea to, instead of having that pipe get overwhelmed and have it back up into people’s basements or come out of manholes in the streets, we designed these structured overflows to purposefully overflow into the streams or into the storm water system," said Cooper, who oversees the consent decree negotiations for the city and the mandatory repairs that resulted.

She said one of the first things the city did following the 2002 agreement was to brick over roughly 60 structured sewer overflow locations. But then, she said, “the sewage had to go somewhere.”

So it poured out of manhole covers or backed up into residents’ basements.

Baltimore is far from alone in dealing with this issue. Consent decrees over sewer overflows are common across the country. In Maryland, both Howard and Baltimore counties have them, as does the Washington Suburban Sanitary Commission, which operates the water systems in Montgomery and Prince George’s counties.

"Just about everybody I know has them if you’ve got an older system," said John Sullivan, the chief engineer at the Boston Water and Sewer Commission, which completed work on a sewer overflow consent decree in the last few years.

For decades, cities didn’t question how their sewers worked, as long as they did, he said.

"I think what happened was because they worked and the problems went away, we didn't spend a lot of time watching out for infiltration and inflow where water that wasn't supposed to be carried into that pipe gets in it. All cities did it," he said. "We were paying attention to the problems at the time, and since the hole in the ground would transport the wastewater, yay us."

In Baltimore, one of the biggest challenges is at the Back River Wastewater Treatment Plant. The plant is the larger of the city’s two sewage treatment plants. It treats sewage from both the city and Baltimore County.

"It all essentially comes to the plant via one really massive sewer — it’s about 12 feet in diameter — called the outfall sewer," Cooper said.

Somewhere around 2009 or 2010, the city discovered that the bottom of the pipe is about five and a half feet below the entrance to the treatment plant.

"The sewage has to back up for about five and a half feet before it can even get into the plant," Cooper said. "That five-and-a-half foot backup spreads out back into the pipe for 10 miles into the city."

That puts a dent in the system’s capacity, making it easier for rain to overwhelm the pipes.

To correct the problem, the city is building a large pumping station to pump sewage into the plant around the clock, plus a storage facility to hold untreated wastewater at times when the volume in the sewer system is high.

The city plans to complete this project by January 2021. By the end of that year, Cooper said, the city will have eliminated 83 percent of the sewage overflowing the system.

But in the meantime, many residents are not just dealing with sewage in their streets, but also in their homes.

Flores’ group, Blue Water Baltimore, which recently joined the consent degree negotiations, wants to see the city provide more assistance to residents dealing with basement backups.

"What we really want to see the city take responsibility to do and what we want to see the regulators require them to do is to have a rapid response to those problems and to go in and to clean it up for homeowners, rather than sort of just leaving them to their own devices," Flores said. "They might not have the resources and certainly not the awareness to clean that up in a way that's safe."

According to Sullivan, Boston offers homeowners grants of up to $4,000 to fix backups caused by problems in city-owned pipes.

But Baltimore doesn’t offer any financial assistance to homeowners to fix sewage backups, something that city and state officials say has been a frequent complaint in public comments submitted on the issue.

The Department of Justice, which collected the public comments, denied WYPR’s request to view those comments.

State Secretary of the Environment Ben Grumbles, whose agency is negotiating the terms of the consent decree with the city, said financial assistance and the timeline of the repairs are both on the table.

"We are looking very closely at the comments that have been filed on the proposed revised consent decree for the city of Baltimore — not just on the timeline, but also on the use of penalties, also on increased accountability and reporting requirements," he said.

Grumbles said he expects the new plan for fixing the sewers to be released sometime this fall.