The six-year-old may have been deliberately thrown in the water from a hire boat by the man in a horrific act of domestic violence, police believe.
"We have uncovered a suicide note and some other evidence drawing us to this conclusion," NSW Police Marine Area Commander, Superintendent Joe McNulty, told 2GB on Monday.
Officers were called to Hen and Chicken Bay at Concord, in Sydney's inner west, at about 11.45am following reports of man's body floating in the river.
A boat owned by a member of the public was used by police to retrieve the 47-year-old, but he was unable to be revived.Â
Reports that a young girl had also been present prompted a widespread search which lasted several hours before her body was also recovered from the water.
Police used CCTV images of the incident from a nearby home to help direct divers to locate the body of the girl.
The man was not known to police and had no recorded history of domestic violence, leaving police with the difficult job of unravelling what occurred.
"We're trying to make sense of this senseless crime," Supt McNulty said.
"We really need to make sense of this, because it is a complex investigation."
Supt McNulty said officers were immediately suspicious as to the circumstances of the incident because life jackets were on board the boat but had not been used.
"It just didn't stack up," he said.
The mother of the girl was notified and present during the search for her daughter.
"At this stage it's horrible but we're wrapping so much care around the victim and the mother that's been left behind," Supt McNulty said.
The girl is the couple's only child, NSW Police Burwood Command Superintendent Christine McDonald told media on Saturday.
"Obviously, a mother in this situation ... it would rock any mother to the core," she said.
A friend of the man had contacted police an hour after his body was located with concerns for the father and daughter's welfare, police said.
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