It's believed the aircraft carrying seven people struck a small limestone outcrop near popular holiday spot Rottnest Island, off the coast of Perth, about 4pm on Tuesday.
The Cessna 208 Caravan 675 plunged nose-first into the water near Thomson Bay, killing pilot James Wong, 34, a 65-year-old Swiss woman and a 60-year-old Danish man.
Investigators are working to retrieve the sunken wreckage to uncover further details about what went wrong during the flight and are particularly interested in obtaining the recording devices that captured its final moments.
"Those few seconds of flight, what went wrong, and most importantly, then what are the sorts of things we can recommend to lessen the likelihood of this occurring again," Australian Transport Safety Bureau Chief Commissioner Angus Mitchell told ABC News on Thursday.
There may also be mobile phones from the passengers on board to help the investigation, Mr Mitchell said.
It will be unclear what state the technology is in until it is assessed at the technical facility in Canberra.
Not only will vision form part of the complex investigation, it will also probe the engine pitch, the aircraft's history, maintenance, the weather and standard operations over Rottnest Island.
"There's a whole range of things to put together to give us a better idea of that sequence of flight and then what went wrong," Mr Mitchell said.
"That will take us time to go through all the evidence."
The seaplane plunged into waters off Rottnest Island soon after it took off. (HANDOUT/ABC IVIEW)
He said once investigators have all the evidence - which could take many weeks - they will begin forming hypotheses of the cause of the crash, and there could be multiple possible scenarios.
"That takes some time for us," Mr Mitchell said.Â
"We need to get these things right if we're to make recommendations that have far-reaching effects."
He hopes there will be a preliminary report within two months.
The owners of the seaplane say they are distraught over the tragedy, particularly the loss of their pilot Mr Wong who was a "deeply cherished" team member.
"Our deepest and sincere condolences are with their families and friends," Swan River Seaplanes company director Kristy Bailey said.
Police divers pulled the three bodies from the wreckage eight metres below the water's surface on Tuesday night after a frantic search during the afternoon.
The survivors include a 63-year-old Swiss man, a 63-year-old West Australian man, a 65-year-old West Australian woman and a 58-year-old Danish woman.
Three bodies were pulled from the crashed plane after a frantic search for survivors. (Aaron Bunch/AAP PHOTOS)
A 200m exclusion zone is in place while investigations and salvage operations continue.
Some wreckage from the seaplane, which broke up during the crash, has been brought ashore.
Witnesses said the plane impact made a huge splash.
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