Southie beaches are cleaner than major urban beaches in five U.S. cities from the East Coast to Hawaii, including Miami Beach, according to a study from the Boston-based group Save the Harbor/Save the Bay.

"We should be proud of the fact that we have such clean water," said Bruce Berman of Save the Harbor/Save the Bay, who led the study comparing water quality tests over the past three years.

South Boston's beaches, City Point, M Street Beach and Carson Beach - where the Deer Island Treatment plant integral to Boston's harbor cleanup sits just across the water - outscored beaches around Virginia Beach, Coney Island Beach in New York City, Santa Monica Beach in California, Waikiki Beach in Honolulu and Miami Beach.

"We didn't cherry pick these beaches. We didn't have to," Berman told the News Service. All of the beaches are near urban areas and affected by stormwater discharge and the study used data measuring the presence of an infection-causing bacteria that is present in feces. Beaches were rated based on the amount of time bacteria was at safe levels.

Miami Beach scored about 97 percent, which is nearly the same as Waikiki and Virginia Beach.

South Boston's beaches collectively scored 99.4 percent over three years and never exceeded the maximum bacterial count during last year's dry summer.

Elsewhere in the city of Boston, beaches are more polluted than the beaches around the country that the group evaluated.

Savin Hill Beach in Dorchester was below the maximum amount of Enterococcus bacteria 92 percent of the time over the past three years. That's a worse score than everywhere except Santa Monica, where the beaches were clean about 83 percent of the time.

Other beaches in the Boston area face worse challenges, said Berman, whose group released the annual Boston Harbor Region Beach Quality Report Card on Memorial Day weekend.

Seawater quality is dependent in part on the amount of wet weather. Heavy rain in the Boston area can sometimes lead to purposeful combined sewage overflows where sewage mixed with rainwater is dumped into waterbodies because the sewer system can't handle it.

Berman said South Boston's water quality was dramatically improved by the 2011 completion of a combined sewage storage tunnel running along the shore by the beaches, collecting water for treatment at Deer Island, which dumps treated sewage outside the harbor in Massachusetts Bay. In 2011, Gov. Deval Patrick said the project's completion "ensures that the shores of Boston Harbor will be among the cleanest urban beaches in the country."

The Massachusetts Water Resources Authority also works to disentangle sewage systems from stormwater systems, and the combined systems are a vestige of the Boston area's older network of pipes.

Overall, Boston Harbor area beaches from Nahant to Hull have improved from 90 percent safety in 2011 to 96 percent safety in 2014, the report card found.

Problems remain at King's Beach along the Lynn and Swampscott shoreline and near the home of Gov. Charlie Baker, which has gone from 73 percent safety to 88 percent over that same period.

"We know what these problems are. We know how to solve them," said Berman, who said the problem at King's Beach appears to be illegal sewage connections.

Around Constitution Beach, an inlet across from one of the runways at Logan International Airport, the city made improvements in the East Boston neighborhood's sewage system resulting in a "rebound," Berman said.

Lawmakers passed bond authorizations in 2014 that could be used for further improving water quality in the Boston Harbor area and Berman hopes the Baker administration puts the money to use.