Beaches in South Boston and East Boston had significantly less bacteria in 2013 than years past, while improper sewage hookups and other pollutants continue to mar the waters at Lynn, Swampscott, Dorchester and Quincy swimming spots, according to Save the Harbor Save the Bay’s third annual report card.

“The biggest story remains South Boston,” said Save the Harbor director of communications and programs Bruce Berman. He said, “Those beaches used to be closed one out of every five days not so very long ago.”

Beaches in South Boston and East Boston had bacteria levels below the state swimming standard nearly 100 percent of the time based on daily testing in 2013. Down the shore, Malibu Beach in a basin near Savin Hill, and Tenean Beach at a Dorchester inlet met that mark 76 and 63 percent of the time, respectively.

King’s Beach on the Lynn-Swampscott line was the next most microbial beach in Metro Boston, clearing the state standards 83 percent of the time. Wollaston Beach in Quincy passed the standard 88 percent of the time, according to Save the Harbor.

Berman told the News Service that efforts in East Boston to ferret out old, illegal hookups that sent sewage into storm drains “really made a difference.” Constitution Beach in East Boston passed the bacteria standard 88 percent of the time in 2012 and 97 percent of the time in 2013, when there was much more rain and therefore greater risk of sewage or other pollutants washing into the harbor.

The House and Senate this year have both passed bills aimed at financing better water infrastructure, and encouraging new techniques for handling sewage with grants. Berman said he wants the Senate to include $20 million in funding for improvements to Metro Boston beaches the House added to an environmental bond bill, and said the money would be spent cleaning up the waters around Dorchester, Quincy, Lynn and Swampscott.

“Tenean and King’s are consistently the worst,” said Berman, who said Tenean is also storm-damaged and “needs to be remade.”

High levels of bacteria can lead to “unlikely” maladies such as an upset stomach, or diarrhea, or ear infections and eye infections, Berman said.

Last year there was “a big regulatory change” where the state required two days of tests exceeding state standards before a red flag would be flown to indicate a beach closure, Berman said. He said the tests take 24 hours to complete and under the previous system where a single test could trigger a closure, the water was often clean by the time the flag was flown.

Berman said the beaches with vastly improved water quality can now have their monitoring reduced to weekly tests, and said, “It’s time to fix the other ones.”

Berman said Tenean likely suffers for its proximity to the Neponset River’s mouth and commercial dog walkers who he said use a nearby park.

King’s is an ironic victim of Lynn’s progress toward cleaning up its sewage system, Berman said. Like most old cities, Lynn had combined sewage and stormwater pipes that would flow to a treatment center unless an influx in rain resulted in an overflow - where the mix of rainwater and sewage gets dumped into rivers or other outflows.

Lynn built a new sewage system that is separate from its stormwater system, but old, illegal hookups continue to send sewage into the stormwater pipes, which flows untreated into the bay, meaning it actually creates more pollution than the old combined system, Berman said. He said, Lynn discovered half the high school toilets were connected to the stormwater system.

“There’s going to be a lot of others,” said Berman, who said both Lynn and Swampscott have “financial challenges” that slow the progress of finding all the illegal hookups.

The Boston Water and Sewer Commission, which works with the Massachusetts Water Resources Authority, used a range of methods to discover how sewage was making its way into the storm drains in East Boston, Berman said.

Full report card: www.savetheharbor.org/Content/beachesreportcard