The pair had taken a rented boat out on Parramatta River near Concord in Sydney's inner west on Saturday when the body of the man in his 40s was found floating in the water just before midday.
His seven-year-old daughter had also gone missing overboard before specialist police divers recovered her body hours later.
Burwood police superintendent Christine McDonald says investigations into the cause of the incident are ongoing.
The man and girl have yet to be formally identified but police said the family was from Westmead, in Sydney's west.
Supt McDonald said whether the incident was deliberate, including if family violence was involved, or an accident was a "definite" line of inquiry.
"There are several lines of inquiry currently under way," she said.
"But can I say from the outset, this is an absolute tragedy for the family and the community on every level.
"We will leave no stone unturned."
A friend of the man contacted police an hour after his body was located, raising concerns for the father and daughter's welfare, police said.
Anyone with information is urged to contact police.
Lifeline 13 11 14
beyondblue 1300 22 4636
1800 RESPECT (1800 737 732)
Men's Referral Service 1300 766 491
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