Nerlin Sarmiento's lawyer, Peter Royal, told court Friday that his client has "very significant mental health issues."
The 32-year-old woman will be held at Alberta Hospital for 30 days while experts determine whether she's fit to stand trial and whether she can be held accountable for the alleged crime.
Police were called Tuesday to an apartment on Edmonton's south side where Sarmiento's son, Omar Jajoy, was found dead.
Results of an autopsy have not been released, although police at one point said the boy appeared to have drowned.
Investigators have also said they believe they have enough evidence to show the death was premeditated.
Sarmiento has been charged with first-degree murder.
The woman, at times crying, stood stiffly in the prisoner's box as several family members sat in the courtroom with their arms around each other.
Royal said his client, who will be on suicide watch while in custody, has been hospitalized twice in the last two years for significant periods of time.
Her husband, Florentino Jajoy, said in a statement Thursday that his wife was under medical treatment and taking drugs for severe depression. But the care she was getting was obviously "wrong" and the health system clearly failed her," he said.
"As a family, our opinion is that she is innocent because she was not responsible for her actions," Jajoy said in the statement.
"She is a loving mother, wife and daughter who put her children's needs before her own."
The couple also has a 10-year-old daughter.
The judge granted a Crown request for an order banning Sarmiento from contacting her husband, daughter and another relative — who are considered key witnesses in the case.
Sarmiento is to be back in court March 15.