Heuermann pleaded not guilty and maintained his innocence.
Heuermann was previously considered a top suspect in the case but at the time of his arrest, investigators said they did not have the evidence to charge him with her death.
The Gilgo Beach task force has been investigating the deaths of 10 people whose remains were found along the New York beach in 2010 and 2011. Most of the victims were sex workers.
In July, police arrested 60-year-old Heuermann for the murders of three women, with police considering him as a suspect in the death of a fourth. Police used familial DNA evidence to help identify Heuermann.
At the time, he was charged with the deaths of Melissa Barthelemy, 24, Megan Waterman, 22, and Amber Lynn Costello, 27. They, along with Brainard-Barnes, were known as the Gilgo Four.
All four women were sex workers; Barthelemy’s family said a man using her phone had taunted the family with graphic details of what he had done to her sexually and said he killed her.
Heuermann was taken into custody and is being held in a Suffolk County correctional facility awaiting trial.
In court filings Tuesday, prosecutors allege Heuermann feared getting caught in the months leading up to his arrest.
He obtained data wiping software in an attempt to destroy evidence on his laptops, phones and other electronic devices, they said. Investigators seized hundreds of devices during their lengthy search of Heuermann’s home that prosecutors say contained troves of bondage and torture pornography.
Heuermann also scoured the internet for phrases that suggested he was afraid of getting caught, including “How does cell site analysis work,” “Gilgo news,” “How cell phone tracking is increasingly being used to solve crimes,” and phrases with the term “Long Island Serial Killer.”
The court documents also detail disturbing Google searches Heuermann was allegedly conducting, such as “autopsy photos female,” “medieval torture of women” and “how I was raped audio.” He also made searches for pornographic material of women tied up.
Heuermann’s attorney, Michael Brown, said afterward that his client has maintained his innocence from “day one” and looked forward to defending himself in court.
He also called into question some of the evidence touted by prosecutors Tuesday, suggesting new DNA analysis connecting Heuermann to the killing was “problematic” since it was being introduced some 13 years after Brainard-Barnes’ body was discovered.
Suffolk County District Attorney Raymond Tierney said in response that more sophisticated DNA testing had allowed investigators to more conclusively determine the hairs found with Brainard-Barnes belonged to Heuermann’s ex-wife and daughter.
He also said the indictment marks the end of the investigation into the so-called “Gilgo four” victims and provides “some small measure of closure” for their families.