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Malary, 31, was reported missing on March 11, according to police.
She last had contact with her family two days earlier and police said she was last seen in the 700-Block of Hinman Avenue.
Her car was found late Tuesday afternoon in a city parking lot at Hinman Avenue and South Boulevard, according to police, who wouldn't comment further.
RELATED: Friends, family continue search for missing Evanston woman and trans advocate Elise Malary
The day she was reported missing, her family and friends gathered to search Rogers Park near the border of Evanston, including near the Howard Red Line stop after her family said they got a tip she was last seen in the area with two men.
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Evanston police said she was last seen near her apartment in Evanston, not far from the border of Rogers Park, and her car was found in a parking lot a few blocks away on Tuesday with no indication of where she may be.
While her apartment had been left unlocked, police said they have found nothing at her home or her car that would indicate foul play.
RELATED: Brave Space Alliance on Chicago's South Side helps trans women of color fighting for their lives
The signs calling for Malary's safe return are still posted around town despite the tragic end to a days-long search.
Her body was recovered along the lakefront in the 500-Block of Sheridan Square near Garden Park in Evanston around 4:30 p.m. Thursday, according to police.
"He saw the legs first, but he was - he was pretty shocked! And, I think he was stunned into silence for the next couple days," said Ruth Lambach.
Lambach said her 19-year-old grandson, who's back home in Switzerland, was walking with a friend on his last day in the states when he found the body.
"Her head was evidently faced down in the water," Lambach. "I know Tristan told me she had socks on, and he couldn't understand that. Because, he was also, sort of, going through his mind and he didn't think it was a drowning. He thought maybe someone pushed her in, or maybe she accidentally fell in."
A woman who advocated for transgender rights is now being remembered for her impact.
Alderwoman Maria Hadden, 49th Ward, tweeted her condolences Saturday, saying in part: "'I'm heartbroken to share that Elise is no longer alive and with us...our community begin to process her loss and our grief. Elise Malary will be missed terribly."
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"The loss of Elise Malary is heartbreaking. My heart goes out to all her loved ones, as well as all of Illinois' transgender community. You deserve to feel safe in your home, and I will continue to do everything in my power to make Illinois welcoming and inclusive for everyone," Governor JB Pritzker said in a tweet.
Attorney General Kwame Raoul said, "The Attorney General's office has lost a member of our family ...." and "May Elise's memory inspire all of us to live authentically and have humanity toward all."
Hadden added that Brave Space Alliance, the first Black and transgender-led LGBTQ+ center on the South Side, has set up a collection to help with Malary's funeral expenses.
Her cause of death and manner are pending, according to the medical examiner.
As tributes begin to pour in, family and friends are planning a candlelight vigil, which they will announce soon.
"It's beyond words. There's nothing one could do about it. It's a tragedy," Lambach.
The Evanston Police Department said they are continuing their investigation and ask anyone with information to contact the Evanston Police Detective Bureau at 847-866-5040.