PORTLAND — The city has agreed to pay more than $53,000 in fines for sewer overflows that contaminated waterways, the U.S. Environmental Protection Agency announced Wednesday.

As part of the settlement of the EPA’s penalty claims, the city also will implement a $45,000 project to prevent future erosion along a 1,000-foot stretch of Dole Brook. Erosion is a form of stormwater pollution that threatens streams and coastal waters.

Since 2007, the city’s sewer system has failed on at least 22 occasions, some of which discharged tens of thousands of gallons of sewer on to roadways and into nearby water bodies.

The EPA found that the city did not do enough to prevent overflows from its sewer system, parts of which date back to the 1800s and are made of clay or brick. Failures occur when lines collapse, pump stations fail or the system gets clogged.

Faced with fines of up to $177,000, the city entered into negotiations with the EPA last November to come up with an “integrated approach” to upgrading its sewer system. The city has allocated $700,000 to conduct a comprehensive study of the city’s sewer system.

EPA Regional Administrator Curt Spalding said in a written statement that sewer overflows are among the largest sources of water pollution in New England.

Sewage overflows carry harmful bacteria, viruses and other pollutants that can cause serious health risks, the EPA said.

“Because of the known health risks associated with discharges of raw sewage into the environment, working with cities and towns to proactively manage sewer systems is one of EPA’s highest priorities,” Spalding said. “The actions called for in this settlement should result in addressing that problem in Portland.”

The EPA rrder requires the city to:

— correct physical deficiencies

— better maintain the sewer system

— better manage high flows that contribute to overflows

— and stop future overflows as quickly as possible.

“While we are pleased to have the matter settled and the penalty amount reduced, the city still faces real challenges managing the many complicated aspects of the Clean Water Act,”  City Manager Mark Rees said in a written statement. “Old coastal cities like Portland face significant financial hardships. Separating our sewer and stormwater system is expensive and has been largely born by the rate payer with little to no support from other agencies. We need an integrated approach that is both environmentally responsible and not overly burdensome to local businesses and residents.”

Rees said the city hopes to wok with the agency to develop a long-range plan to address the sewer and stormwater in a manageable way.