Tarrin-Macen O'Sullivan was discovered after emergency services responded to a call about a child drowning in August, 2021.
Police on Friday said it would be alleged the boy was dead before he entered the disused pool at the Munbura residence near Mackay.
His 46-year-old mother was the only one home with him at the time, Detective Superintendent Darrin Shadlow said.
She was charged after a "very complex" investigation featuring medical and biomechanical specialists.
"It was a disused pool in the backyard of the property. It only had a small amount of water in it," Det Shadlow told reporters.
"We believe we can prove the child was deceased before entering the pool. We can show the child didn't ingest water."
The boy had not been dead long before his mother called emergency services, Det Shadlow said.
"The quick work by investigators who attended that scene initially showed that something wasn't right," he said.
The boy's father did not reside at the property at the time and was "distressed and distraught" when told of the arrest on Friday.
"It's obviously a very difficult investigation," Det Shadlow said.
"The investigation into a child's death is something that is extremely challenging for all police ...and for the family as well."
The woman was to appear in Mackay Magistrates Court on Friday.