State Police said the facility will be closed all day Friday.
The underground garage is used by state government employees who work in the Statehouse complex.
It's located less than 200 yards from the banks of the Delaware River, and is prone to flooding when the river rises.
The Delaware is expected to reach flood stage in the Trenton area on Friday following the region's second major rainstorm in five days.
Workers who normally use the garage will be able to park at the Sun Bank Arena across town and take shuttle buses to the Statehouse.
