Police said the dinghy was travelling south between Sovereign Island and Paradise Point at 3.30pm when the vessel struck an unoccupied yacht anchored in waters off The Esplanade.
The skipper on the dinghy was taken to Gold Coast University Hospital with life-threatening head injuries.
Queensland Police acting superintendent Scott Knowles told ABC Radio the man was "impaled" by a large piece of wood.
The 47-year-old from the Gold Coast remains in a critical condition.
Two passengers were on the dinghy at the time, including a 41-year-old man from Mount Warrant Park and a 56-year-old man from Mount Nathan, were not physically injured.
The pair is assisting police with their enquiries.
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