When Karina Vetrano was found slain last August in Spring Creek Park, a small, muddy puddle near her body that never seemed to dry up even in the most severe summer heat puzzled detectives.

Investigators noted the seemingly innocuous detail at the time but didn’t give the tiny body of water much more thought until this past weekend. Chanel R. Lewis, 20, the Brooklyn man accused of killing Vetrano as she jogged in the park Aug. 2, described the same puddle during interviews with detectives, police said.

Lewis’ recollection about the puddle, according to a law enforcement source familiar with the case, proved to investigators he had indeed been in the park at the time of Vetrano’s killing, which police said he confessed to committing.

After NYPD detectives interviewed Lewis twice and the medical examiner confirmed his DNA matched the genetic material found at the crime scene, he was formally charged Sunday with one count of second-degree murder for the strangulation of Vetrano. He was ordered held without bail and is expected in court on Feb. 21. Officials said more charges may result.

In his statements to cops, Lewis indicated that his alleged attack on Vetrano was an impulsive act, sparked by problems at his family home in East New York, the source said, and not so much by anger at women in general, as has been reported. Lewis said that as he got near Vetrano, he yanked off his ear buds and attacked her, the source noted.

The diminutive Vetrano, who barely weighed 100 pounds but was an avid jogger, tried to fight off her attacker, scratching the person and grabbing at weeds as she was dragged to the spot where she died. Police said her assailant tried to complete a sex act but apparently didn’t. Cops were surprised that Lewis didn’t turn out to be a large man.

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“He wasn’t the hulk we expected,” the source said.

As police escorted Lewis Sunday, he answered “no,” when photographers pelted him with questions about whether he committed the crime.

DNA found under Vetrano’s fingernails gave police enough material to ultimately match it with a sample Lewis voluntarily gave to investigators, NYPD chief of detectives Robert Boyce told reporters on Sunday.

“You got to remember, Karina helped us,” Boyce said. “She had DNA under her nails, she had much DNA on her back, she had more DNA on her cellphone.”

Lewis was identified as a possible suspect last week after Lt. John Russo, who works for Chief of Detectives Robert Boyce, recalled a complaint from May in which Howard Beach residents said a suspicious man had been seen in the back yards of some homes. Russo spotted Lewis around May 6. Patrol officers at the time noted Lewis’ name and address before sending him on his way since they hadn’t observed a crime, officials said.

About 10 days ago, investigators located the patrol report. Thursday, detectives interviewed Lewis at his Essex Street home where he told them he went to Howard Beach in May because he liked the food, the source said. Lewis also volunteered to give cops his DNA sample, one of six collected in the case. When Lewis’s DNA matched that found on Vetrano, cops took him into custody last Saturday.

“This case was very similar to a needle in a haystack, because this individual had no prior arrests” Boyce told reporters Monday during a briefing on crime with NYPD Commissioner James O’Neill and Mayor Bill de Blasio.