Ashley Diaz, 28, could face life in prison if convicted of second-degree murder after prosecutors say her daughter was found unresponsive Monday in their apartment in Far Rockaway.
Kevasia Edwards was pronounced dead at the hospital.
The autopsy revealed evidence of violent impacts to the toddler's head and body.
"The defendant has been charged with causing the death of her own child, a defenseless 2-year-old girl who suffered greatly in her short life," District Attorney Richard Brown said. "The actions of the defendant are totally incomprehensible."
New York City's Administration for Children's Services has investigated the family before.
"It didn't work," a neighbor said. "It was too late. She was gone. She was gone."
On Tuesday, detectives returned to the building where family lived on the sixth floor. Kavasia has four brothers, ages 10, 6, 4 and 3.
George Frank is a security guard there, and he told Eyewitness News he used to always see Kevasia with her mom.
"Cute little girl, very, very nice," he said. "Always called me papa here, so when I heard it hurt me a little bit."
Investigators say that when they found the little girl, she had bruises around her mouth and broken ribs.
Sources tell Eyewitness News that ACS officials received four complaints -- three against Kevasia's mother and one linked to the child's father, since 2011 and all determined to be unfounded. Still, this wasn't Diaz's first run-in with police. She was arrested in 2008 for assault and 2011 for menacing, in addition to three other incidents in her record that are sealed.