The break-in at the facility, located off of Bolinas Road, happened between 5 p.m. Monday and 9 a.m. Tuesday, Heying said.
Someone pried open the lock on the garage, then broke the trucks' windows, Heying said.
The thief used tools to disassemble one of the locked mounts that secured a Rock River Arms LAR-15 semi-automatic rifle, and forced open the other locked mount that contained the second rifle, Heying said.
Some ammunition also was taken, he said.
The sheriff's office provides services for land in the Marin Municipal Water District, Heying said.
The intruder went through other vehicles in the garage, but it's not clear whether anything was taken, Heying said.
The thief had to climb a fence to get to the garage, and would have had to drive to the remote area, Heying said.
So far, there is no suspect description in the case. Anyone who is contacted to purchase the rifles, or who has information about the case, is asked to call the sheriff's office at (415) 499-7265 or Bay Area Crime Stoppers at 800-222-TIPS.