The vandalism that led to the arrest was of the school's "snack shack," a storage container used to store candy and snacks sold at athletic events.
The snack shack was broken into over the weekend of March 23, and food, cash and supplies worth $180 were stolen.
Police found out that a 16-year-old student at the school may be responsible, and after interviewing the suspect, police said he admitted to the burglary.
After further investigation, police determined that two of the student's friends, identified as Kyle Collins, 19, and Kyle McGauley, 18, were allegedly accomplices.
Police interviewed the three and said they admitted to numerous burglaries and vandalisms in the Terra Linda, Marinwood and Santa Venetia neighborhoods.
They were all arrested on suspicion of the school burglary and police said that they will be charged with additional crimes.
Officers also searched McGauley's car and found a pellet gun and ammunition and police said that McGauley is also suspected of bringing the weapon onto school grounds.
McGauley and Collins were booked into Marin County Jail and their bail was set at $15,000. The 16-year-old student was booked into Marin County Juvenile Hall.