The 25-year-old man, whose name has been withheld to protect the child's identity, was charged on Thursday with aggravated assault after his baby was found unconscious one day earlier.
The infant, who was not yet two months old, was rushed to hospital in nearby Buckingham, Que., before being transferred to a hospital in Ottawa with symptoms of shaken baby syndrome.
She remained in critical condition until she died from her injuries on Friday night, police said.
Last week, the Crown opposed the father's release and he remained behind bars over the weekend.
He returns to court on Monday morning hoping to receive bail, but he could face further charges pending the results of an autopsy.
Marc-André Cayen, the lawyer representing the baby's father, said he doesn't have a criminal record and had never been arrested before.