Police responded to reports of a plane crashing into the water at Long Bay near Murray Mouth, about 85 kilometres south of Adelaide, shortly before 4.30pm on Friday.
The pilot, a 57-year-old man from Morphett Vale, as well as his two passengers, aged 18 and 19, were found deceased.
Efforts to retrieve the wreckage were hampered by rough seas with a police helicopter, firefighters, SES and private sea operators involved in the operation.
"The wreckage of that single engine Cessna 210 aircraft has been brought into shore near the Murray Mouth," Senior Constable Rebecca Stokes told ABC Radio Adelaide.
"Tragic news for three families in South Australia today."
The Australian Transport Safety Bureau has commenced an investigation into the cause of the crash and is appealing for anyone with footage of the incident to come forward.
"Investigators will also interview witnesses and involved parties, collect available video footage and any recorded flight tracking data," the agency said in a statement.
A resident of nearby Goolwa told the ABC the scene near the crash was "chaos".
The crash site is a remote beach but a popular fishing spot as it marks the spot where the Murray River meets the Southern Ocean.
Police will prepare a report into the crash for the coroner.
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