This could be the dirtiest part of New York City to take a dip.

The waters at three beaches in southeast Brooklyn were festering with so much fecal bacteria, they were deemed unsafe for swimming on 101 days over the past two summers, according to city Health Department records.

The filthy surf plagued the roughly mile-long stretch covered by Kiddie, Manhattan and Kingsborough Community College beaches, which are concentrated around Rockaway Inlet.

They accrued more than triple the total bacteria warnings issued at the city’s seven other public beaches. Ocean beaches have less stagnant water than inlet beaches.

The Health Department attributed the bacteria uptick to “increased rainfall.”

A clean-water advocate explained that the city has 460 points along its shoreline where about 27 billion gallons of raw sewage and storm water are dumped into New York Harbor every year when combined sanitary-storm sewers overflow during heavy storms.

“That’s the product of hundreds of years of overdevelopment in the city,” said Dan Shapley, the water-quality program director for Riverkeeper. He explained that certain city sewer designs date back to “when people were dying of cholera and the goal was to get [the sewage] out and away from the neighborhood as fast as possible.”

The Health Department measures the level of Enterococci bacteria — which live in the intestinal tracts of warm-blooded animals and can cause vomiting, diarrhea and infections — every week or bi-weekly at the city’s eight public and 17 private beaches. The beaches are required to post warning signs when the daily bacteria count exceeds 104 colony-forming units per 100 milliliters of water, and they close when the five-week average tops 35 units.

In 2015, there were zero advisory days at Manhattan and Kiddie beaches; Manhattan had two days in 2016 and 10 last year, while Kiddie had 15 in 2016 and 17 in 2017. Kingsborough Beach had 15 warnings in 2015, which went up to 30 in 2016 and 27 in 2017.

Still, swimmers at Kiddie Beach, where there was a bacteria advisory Friday, seemed unfazed by the filth.

“I grew up in this water, and I have never been sick from the water. I have never had any health issues after swimming and neither have my three children, so I’m not concerned about it at all,” said Jennifer Avena, a beach manager.

“I survived Hurricane Sandy and lost everything, so nothing really fazes me anymore.”

If you remove Manhattan Beach and its 10 no-swimming days, New York City’s seven other public beaches — Orchard, Coney Island, Rockaway, Cedar Grove, Midland, South and Wolfe’s Pond — are relatively sparkling. Last summer they had 12 warning days combined, and none were closed.

“The city’s public beaches are safe and clean, and they’re open for the season,” said Health Department spokeswoman Danielle De Souza.

“Occasionally, heavy rainfall can impact water quality. New Yorkers should sign up for ‘know before you go’ alerts and check signs posted at the beach to learn about any swimming restrictions,” she said.