The Australian Safety and Transport Bureau has started recovery and examination of wreckage from the crash site near the popular holiday spot Rottnest Island, off the coast of Perth.
It is believed the aircraft carrying seven people struck a small limestone outcrop soon after it took off about 4pm on Tuesday.
The Cessna 208 Caravan 675 nosedived into water near Thomson Bay, killing pilot James Wong, 34, a 65-year-old Swiss woman and a 60-year-old Danish man.
It is estimated understanding the cause of the crash will take months.
Bureau investigators are working to retrieve the plane's recording devices that involve flight tracking, engine performance data and any other devices onboard.
What remains of the aircraft can be clearly seen in the crystal clear waters of Thomson Bay as it harrowingly rests on the seabed.
Once the on-site examination is finalised, the wreckage will be taken to a Perth facility for further scrutiny.
"During this time, investigators will identify and secure any relevant components for further analysis at the ATSB's laboratory facilities in Canberra," bureau chief commissioner Angus Mitchell said.
"We also continue to seek reports from witnesses, in particular anyone who may have footage of the aircraft at any stage of the accident sequence, or in the immediate aftermath."
The seaplane plunged into waters off Rottnest Island soon after it took off. (HANDOUT/ABC IVIEW)
Should investigators discover a critical safety issue during their seaplane probe the bureau will notify relevant stakeholders, Mr Mitchell said.
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."
He said once investigators had all the evidence - which could take many weeks - they would 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.
"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.
Rottnest Island is a popular tourist destination off the coast of Perth. (Aaron Bunch/AAP PHOTOS)
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.
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.
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