The waters off Havens Beach in Sag Harbor Village contained the highest amount of enterococcus bacteria of any East End bathing beach sampled on May 6 by the Surfrider Foundation, nearly 25 times more than the level considered unsafe by federal regulators. The test took place after an entire week of heavy rains, said Colleen Henn, the foundation’s clean-water coordinator, who was not surprised by the results. “Many of our bay, pond, creek, and even ocean locations feel the effects of stormwater runoff,” she said. Havens Beach lies at the bottom of a natural watershed, and the contamination of its water has been a concern for decades. In 2013, the village installed a filtration system within an existing drainage ditch to help mitigate the amount of human and animal waste that flows to the site, particularly after a heavy rainfall. “Mismanaged wastewater, pet owners not cleaning up after their pets, bird waste, and excess irrigation all play a part in water quality pollution,” said Ms. Henn.The high level of bacteria found in the latest test results left residents wondering if the village’s filter is functioning properly.At a meeting of the village’s harbor committee on Monday, Stephen Roache, president of the Ninevah Beach Property Owners Association, said, “The town is spending millions of dollars on something that does not work, so we need to have that addressed by this community or by the town.”John Parker, a committee member, said the system’s “smart sponges,” which reduce bacteria levels, may need to be replaced, which would cost $60,000 and “as far as I know, they haven’t been replaced, and they’re probably not working properly now.”Mary Ann Eddy, the chairwoman, did not agree with that assessment. “The bacteria levels were far higher before the installation of the filter,” she said. “I don’t know that there’s any system that’s going to prevent us from having bacteria in the water after the kind of heavy rains that we’ve been having.”Despite the high levels of enterococcus found at Havens Beach in the May 6 test, Ms. Henn said that “historically, it is not one of our sampling locations of highest concern.” Still, she advised the public to avoid contact with the water for one to three days after a downpour.