A clean harbor advocacy group is giving strong grades to most Boston Harbor beaches in its second annual report card, but it is also highlighting some problems.
More than half of the 15 beaches graded by Save the Harbor/Save the Bay scored either an A or A-plus in the report released Sunday. That means they were open at least nine out of 10 days last year.
Three beaches, two in Revere and one in Winthrop, did not shut down once.
But King’s Beach, which straddles Swampscott and Lynn, and Tenean Beach in Boston filled out the bottom of the list, with Tenean Beach closed once every five days because of high fecal bacterial levels, which can cause illness. Still, those two beaches both improved from the previous year.
Bruce Berman of Save the Harbor/Save the Bay said last year’s dry weather, which reduced the flow of dirty storm-water runoff, as well as pipe repairs helped continue a turnaround for harbor beaches.
The foul conditions in local waters were once famous enough to be the focus of the Standells’ Boston tribute song, ‘‘Dirty Water.’’ But years of extensive cleanup, costing billions, has produced years of cleaner beaches.
‘‘Just 25 years ago, these beaches were awash with human waste,’’ Berman said. ‘‘We should be proud of what we’ve done and be prepared to finish the job.’’
This year’s report card, based on analysis of thousands of state water samples taken in 2012, said Winthrop Beach and Revere Beach and Short Beach in Revere were open every day of the beach season, between Memorial Day and Labor Day.
State Representative Kathi Reinstein of Revere said the perfect scores boost tourism and development and are important in a community where everyone calls their local beach ‘‘my beach.’’
‘‘There is incredible personal ownership of the beaches you grew up on,’’ she said. ‘‘And when it doesn’t look good . . . we hear about it.’’
Nantasket Beach in Hull, which had a perfect score in 2011, dropped slightly in 2012, as it passed 98.3 percent of the bacteria tests.
Three South Boston beaches passed 99 percent of their bacteria tests, after a massive project completed in 2011 routed storm water into a treatment plant instead of letting it empty onto the beaches.
The lowest grades went to Tenean Beach in the Dorchester section of Boston, which was open about 81 percent of the time in 2012. Next lowest was King’s Beach, which passed 86 percent of its tests.
Both results were better than in 2011, but Berman said improvement is needed.
John Sullivan, chief engineer of the Boston Water and Sewer Commission, said steady progress at Tenean Beach should follow an ongoing effort to ferret out illegal sewer connections that can drain into the ocean.
That tedious and difficult job should be done by next year, he said. He added that some waste cannot be controlled, such as what is produced by birds, squirrels, and other critters and carried by rainwater to the beach.
‘‘There’s no assurances ever that nature doesn’t cause a violation,’’ Sullivan said.
Dan O’Neill, director of the Lynn Water and Sewer Commission, said illicit sewer connections are a problem for King’s Beach, too. But he also said correcting flaws in testing will help. For instance, eliminating improper sampling at the mouths of pipes at King’s Beach — which skews results toward higher concentrations of pollution — should lead to major improvements, he said.
‘‘The results are going to be significant,’’ he said.
The report card also looked at the effectiveness of a warning system in which posted red flags indicate the beach is unsafe for swimming and blue flags signal all is well. It found the flags too frequently lag behind actual conditions on several beaches, mainly because the water tests take 24 hours to process.
Berman said state officials are phasing in a new system that uses scientific modeling to close beaches immediately, based on historical data of when certain amounts of rainfall have caused that beach to close in the past.