The incident on December 30 occurred during a “thrill ride” on the river, leaving the driver of a recreational boat seriously injured, a Maritime NZ spokesperson said.
The decision to file charges, under the Maritime Transport Act 1994, followed a thorough investigation.
A police spokesperson told the Otago Daily Times that the collision occurred at about 2pm near the Clutha River Bridge in Albert Town.
It left one person with a serious back injury stranded on an island in the river with about six others. A helicopter was called to retrieve them, and the injured person was flown to Dunedin Hospital.
There is a hearing scheduled in the Queenstown District Court next month over the matter.