Police divers and a barge equipped with a small crane arrived at the scene early on Thursday morning local time to begin lifting the wreckage out of the water, about 25 miles north of Sydney.
The plane had lost its wings and the propeller, cockpit and front section of the fuselage had been crumpled.
The remains - which also include the aircraft's landing floats - will now be examined, and investigators hope to also find personal phones or other electronic devices which may help piece together what happened.
Among those who died in the crash, which happened shortly after takeoff, was 58-year-old Richard Cousins - the chief executive of British catering firm Compass Group Plc - and four members of his family.
Those were his sons Edward and William Cousins, 23 and 25, fiance Emma Bowden, 48, and her daughter Heather Bowden, 11.
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Sydney Seaplanes, which operated the flight, has so far declined to comment on the crash, but its director Aaron Shaw has told reporters the engines on its planes were regularly replaced, and the motor on the crashed aircraft had only flown for around 200 hours.
The business has operated without mishap since 2005, but air crash investigation records show a plane with the same serial number - a DHC-2 de Havilland Canada - crashed and killed a pilot during use as a crop duster in 1996.
The records say that the plane likely stalled during windy conditions and a spokesman for Australia's Civil Aviation Safety Authority said it later was repaired and re-registered for service.
Pilot Gareth Morgan, 44, was also killed in the crash on Sunday.
England cricket fans paid tribute to those killed in the crash before their final match-up with their Australian counterparts in "The Bashes" - a five-match series taking place alongside the Ashes.
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The Barmy Army wore black armbands and held a minute's silence before the game, which co-founder Paul Burnham said was "the right thing to do".
"It was a horrible accident, and we felt it deserved our recognition that an Englishman here following the cricket had died in these circumstances," he added.
Mr Cousins had planned to attend the fifth Ashes test at the Sydney Cricket Ground, which got underway on Thursday.
