The incident at Mornington Peninsula, which was captured on video by a passenger, allegedly concerned the jet ski rider intentionally spraying the occupants of the boat with water earlier than rushing off on Monday afternoon.
The 16-year-old boy will probably be charged with harmful operation, exceeding 5 knots inside 50 metres of one other vessel, and failing to take care of security gear.
Zara Learn, 13, who was on the boat on the time of the incident, instructed 9News that it was a "horrifying" expertise.
"It was fairly scary," she stated.
Water Police Squad Performing Sergeant Michael Greenwood stated police had a "no tolerance" method to harmful behaviour.
"In case you interact in this sort of behaviour, keep in mind our strike groups are usually not far-off," he stated.
"You can be caught up with."
The teenager will face a magistrates' court docket at a later date.
The fees include a compulsory six-month lack of licence and could be accompanied by hundreds of dollars in fines.