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A settlement filed Thursday in U.S. District Court compels the Metropolitan St. Louis Sewer District to rebuild that system over the next two decades — at a cost of $4.7 billion — to help clean up local rivers and improve public health.

The MSD "will essentially redesign and rebuild its far-flung system of pipes, pumps and plants," Karl Brooks, the Kansas City-based regional director for the Environmental Protection Agency, said at a news conference Thursday afternoon in St. Louis. For too long, he said, the city has treated local rivers and streams as "a dumping ground for sewage."

Formally known as a consent decree, the settlement resolves a lawsuit the EPA filed in 2007 against the district alleging violations of the federal Clean Water Act. It specifically targeted the billions of gallons of raw sewage flowing annually into rivers and streams and thousands of sewer overflows into basements, yards and parks that occur during heavy rains.

Those problems won't be completely eliminated, but officials said they should be significantly reduced by the agreement announced Thursday.

Ignacia Moreno, assistant attorney general for the Department of Justice's Environment and Natural Resources Division, called the agreement "an historic milestone" for the city and the region, one that "requires MSD to make improvements to its sewage treatment and collection system on an aggressive, but reasonable 23-year schedule."

The area's sewer system, the nation's fourth-largest, collects and treats wastewater across 525 square miles in St. Louis and St. Louis County. It contains more than 9,600 miles of pipe, enough to stretch from St. Louis to Seattle more than five times.

Just like the system itself, the scope and cost of the work required by the consent decree are enormous.

Brooks said the sewer rehabilitation will constitute the largest public works project in St. Louis' history, and the "nation's most significant sewer transformation project ever."

Not only will it produce environmental and health benefits, but also economic benefits equivalent to the construction of the U.S. interstate system in the region 40 years ago.

Work to be performed over the next two decades includes constructing three large storage tunnels ranging from two miles to nine miles long and expanding the treatment capacity at two wastewater treatment plants.

In all, projects are designed to reduce overflows into streams and rivers by 13 billion gallons annually, officials said.

The consent decree especially requires the MSD to:

• Eliminate bypasses that allow raw sewage to flow into streams or the ground during storms. The district has about 200 such discharge points, and must remove 50 of them by the end of 2012.

• Invest $100 million on green infrastructure, such as rain gardens, to reduce and slow down storm water. Much of the work will be focused in the city's poorest neighborhoods.

• Spend $230 million to alleviate flooding. Doing so will reduce the amount of sewage in the oldest part of the sewer system, which is overwhelmed during rainstorms and causes sewage to flow into the Mississippi River and River Des Peres.

• Invest $30 million to replace or line failing sewer pipes in minority and low-income neighborhoods.

• Pay a $1.2 million civil penalty.

The MSD, which has already agreed to the consent decree, has spent $2.3 billion over the last 20 years to eliminate more than 300 sewer overflows, and doesn't dispute the need for additional investment.

"The true question is how quickly this work is completed, which is the driver behind continued increases in monthly sewer bills," the district said in a statement.

The sewer system overhaul will come at a steep price but one the EPA officials say is "doable."

The MSD is proposing to raise sewer rates about 13 percent annually over the next four years to pay for the first phase of the work.

The settlement must be approved by a judge following a 30-day public comment period.

The Missouri Coalition for the Environment, which intervened in the lawsuit, also has agreed to the consent decree. But the state of Missouri has not.

Attorney General Chris Koster has so far been unwilling to sign the agreement because it hasn't resolved all issues with the MSD, said Nanci Gonder, a Koster spokeswoman. Neither she nor the MSD elaborated on what those differences are.