A construction crew works about a mile into the new tunnel being constructed on the Clean Rivers Project. It is D.C. Water’s program to reduce sewer overflows into the Anacostia and Potomac rivers and Rock Creek. (Jonathan Newton/The Washington Post)

The District’s water and sewer utility has sued the Environmental Protection Agency, alleging that it improperly calculated new limits on the amount of E. coli that the region’s sewage treatment facility may discharge into the Potomac River.

D.C. Water says the EPA didn’t account for the fact that the Blue Plains Advanced Wastewater Treatment Plant can have spikes in E. coli levels when rain water rushes into the plant during storms. In addition to being in human waste, E. coli is found in animal waste that runs off lawns with rain water.

The lawsuit filed Monday in U.S. District Court is being closely watched by sewer utilities across the country because they also must abide by limits on E. coli as specified in the permits that govern their wastewater treatment facilities.

D.C. Water said flaws in how the EPA calculated the new daily limits for its upcoming permit renewal would result in “unreasonable mandates” that would require as much as $1 billion in upgrades to the Blue Plains plant in Southwest D.C. Blue Plains, the largest such plant in the world, treats sewage for more than 2 million people in the District, and parts of suburban Maryland and Northern Virginia.

D.C. Water did not make anyone available for an interview Wednesday. In written responses to e-mailed questions, spokesman John Lisle said the previous limits required D.C. Water to “control” E. coli but allowed for “natural fluctuations” in bacteria levels during rain storms.

“The plant’s treatment performance already meets or exceeds that required to meet water quality standards,” Lisle wrote. “The revised requirement would not lead to measurable improvements to water quality."

Environmental activists say wastewater treatment plants are a major contributor of E. coli and other pathogens in the Potomac and other waterways. While most E. coli bacteria are harmless and often found in healthy people’s digestive systems, a toxic strain in waterways can make swimmers, rowers and other recreational users severely ill if they swallow water.

Like many older sewer utilities in the U.S., D.C. Water has been under scrutiny for years for the amount of pollution its sewer system sends into local streams and rivers. D.C. Water has a particular problem because older parts of its sewer system, built in the late 1800s, also carry stormwater and get overwhelmed in heavy storms. That causes untreated sewage to overflow directly into creeks and rivers before reaching the treatment plant.

Phillip Musegaas, legal director for the Potomac Riverkeeper environmental group, said D.C. Water should be able to sufficiently treat water before Blue Plains discharges it into the river.

“That’s a large, state-of-the-art plant that they’ve invested a lot of money in,” Musegaas said. “There’s no reason they can’t meet the daily standard.”

As part of a 2005 legal settlement with the U.S. government, D.C. Water has spent $1.5 billion to reduce sewer overflows into creeks and rivers. That includes building massive tunnels beneath the city that will hold rain water until a storm passes and the water can be pumped to Blue Plains. Other work includes expanding capacity at Blue Plains to better treat the sewage-rainwater mixture during heavy storms. The 20-year Clean Rivers Project is estimated to cost $2.6 billion total. The long-term construction plan was based on the previous E. coli limits.

George S. Hawkins, D.C. Water’s general manager and a former lawyer for the EPA, said the utility was forced to file the suit because, after some back-and-forth, the EPA issued the new final limit before allowing D.C. Water to comment on it.

EPA spokeswoman Laura Allen said Wednesday that the agency doesn’t comment on pending lawsuits. However, in a December 2014 letter setting the new limits, the agency said it needed to revise the 2004 bacteria limits because of findings in two legal cases, in 2006 and 2009. In those cases, environmental groups successfully argued that E. coli levels in water discharged from sewer systems should be based on daily maximums. Previous limits allowed for an average amount of the bacteria found over five days during a 30-day period.

Amanda Waters, general counsel for the National Association of Clean Water Agencies, said her organization found a “technical flaw” in how the EPA calculated the new daily limits.

“We’re watching this closely,” Waters said. “We need to see how EPA reacts to this lawsuit. If they really defend this practice, then it’s no longer a technical flaw. Then it appears to be a policy position, and then we will be concerned.”

Tighter E. coli limits for Blue Plains would have “huge ramifications” for D.C. Water, she said, because the utility would have to rework its long-term plan to reduce pollution in waterways. The new limits, she said, don’t properly take into account “anomalies” that can occur in bacteria levels when heavy rains overwhelm a system.

“You don’t want to spend a huge amount of resources to address something that happens on a more sporadic basis,” Waters said.

Environmental activists said stricter limits on E. coli better protect public health because it’s considered the best indicator of potentially dangerous pathogens found in insufficiently treated human sewage.

“It will be difficult [for D.C. Water] because now they’ll have to meet a new limit,” said Jon Mueller, vice president of litigation for the Chesapeake Bay Foundation. “But the EPA can require more limits to ensure water quality standards are obtained.”

Musegaas, of the Potomac Riverkeeper, said the previous E. coli limits that used a daily average rather than a daily maximum were insufficient.

“People don’t swim in ‘average’ water,” Musegaas said. “People go out when they go out. If water isn’t clean for people daily, then you’re not protecting public health. You’re just protecting it most of the time.”