Josiah Brown passed away Sunday at 10:16 a.m. after his aunt allegedly pushed the boy into the water Monday.
Victoria Moreno, 34, was arrested Monday in the 700-block of East Grand Avenue, Chicago police said Wednesday morning.
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Moreno did not attempt to rescue the boy, CPD said.
She appeared in bond court Wednesday afternoon, where a judge denied her bond. Her next court appearance is scheduled for Friday.
According to prosecutors, the 3-year-old was also with Moreno during a previous incident a week earlier in which she allegedly stole the family's car and took her two nieces and nephew to Navy Pier, but the older niece called relatives to get them.
Moreno has additionally been ordered to have no contact with her family.
His family was around the child's bedside on Tuesday at Lurie Children's Hospital. They are asking for privacy, and his grandfather, Dan Brown, said they need "a lot of prayer right now."
"Everybody's prayer helps," Brown said. "God makes things happen. That's what we are banking on right now."
Police said the child went tumbling several feet into the lake, nearly drowning about 1 p.m. Monday afternoon near the north end of Navy Pier. He was walking with his aunt on the path next to the lake, before going into the water.
Divers with the Chicago Fire Department pulled the child to dry land before rushing him to the hospital in full cardiac arrest.
Brown described his grandson as "just a bundle of joy" who is "full of energy, wants to do everything" and "loves his dad."
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"I just want to give thanks to those who were there to respond," Brown said. "The situation is bad, but it could have been worse, so we have a praying chance that he makes it through, and that's all we are hoping for at this point."
Investigators said the boy spent hours undergoing treatment as police remained at Navy Pier, working to determine what exactly happened.
"As with incidents involving children, these are difficult circumstances, and, again, we ask that you keep the family in your thoughts," said CPD Deputy Chief Gabriella Shemash.
At bond court Wednesday, prosecutors told the judge the boy is not expected to survive and charges could be upgraded.
The relative initially told responding officers she was only a witness to the drowning, then claimed she was holding the boy's shirt and let him fall into the water, according to a source with knowledge of the investigation.
Surveillance video shows the woman pushed him toward the edge of the pier and tossed him into the water, the source said. The boy wasn't expected to survive, the source said.
A witness said they noticed the boy running around seemingly unsupervised just before the incident.
Other witnesses on the scene described it as an odd situation, with the aunt just standing by while the child was in the water.
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The woman who called 911 explained the horror of the entire situation.
"It's one thing to see him having been in there, and it just brings it to a whole new level to know it was intentional," Ashton King said. "I have a son who is about that boy's age. I relive the image every day. He just looked so panicked and scared, and to think that somebody he trusted put him in that position is horrendous."
The woman said she wanted to jump in and help, but had to consider the factors of doing so while helping first responders get to the correct location.
She and her friend threw a lifesaver into the water as another man was already down there trying to help.
The Illinois Department of Children and Family Services said there is no prior contact regarding this child, and the department is investigating.
Her charges could escalate now that the child has died.
Sun-Times Media contributed to this report.