A teenage jet ski rider who allegedly rode dangerously close to a boat at a Melbourne beach earlier this week will be charged by police.

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.

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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.

"If you engage in this type of behaviour, remember our strike teams are not far away," he said.

"You will be caught up with."

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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.