The 41-year-old man from Sydenham in Melbourne's north west died about 1.20pm on Thursday at Skenes Creek.
A family member tried to help the man, but was unsuccessful, while the boys aged eight and 12 were rescued safely.
The two boys were taken to Geelong University Hospital in a stable condition.
Skenes Creek is a 200km long beach south west of Melbourne on the Great Ocean Road.
Police are preparing a report for the coroner.
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-With AAP

