The incident at Mornington Peninsula, which was captured on video by a passenger, allegedly involved the jet ski rider deliberately spraying the occupants of the boat with water before speeding off on Monday afternoon.
The 16-year-old boy will be charged with dangerous operation, exceeding five knots within 50 metres of another vessel, and failing to maintain safety equipment.
Zara Read, 13, who was on the boat at the time of the incident, told 9News that it was a “frightening” experience.
“It was pretty scary,” she said.
Water Police Squad Acting Sergeant Michael Greenwood said police had a “no tolerance” approach to dangerous behaviour.
Read Related Also: How Nicole Kidman's 'nepo baby' niece Lucia Hawley is copying her famous aunt's glamorous red carpet
“If you engage in this type of behaviour, remember our strike teams are not far away,” he said.
“You will be caught up with.”
The teen will face a magistrates’ court at a later date.
The charges come with a mandatory six-month loss of licence and can be accompanied by thousands of dollars in fines.