Immediately following the activation, the battalion simultaneously deployed to the big island of Hawaii in direct support of 3rd Marine Regiment, aboard the USS Bonhomme Richard, and to Pearl Harbor to conduct security operations in support of nuclear submarine operations.

On 1 November 2008, just 121 days old and the youngest battalion in the United States Marine Corps, CLB-3 was designated the Logistics Combat Element (LCE) of the Special Purpose Marine Air-Ground Task Force – Afghanistan and deployed to Camp Bastion, a military base run by the United Kingdom in Southern Afghanistan.

From November 2008 to May 2009, the battalion conducted combat operations in Southern Afghanistan providing all six functions of logistics: transportation, engineering, maintenance, supply, health services, and services to all Marine and NATO forces in Southern Afghanistan.

On 8 December 2021, CLB-3 responded to the Red Hill Water Crisis aboard Joint Base Pearl Harbor-Hickam where it provided shower and laundry services to affected families and set up no less than seven water distribution points throughout the base and surrounding military communities.

As part of Task Force Kuleana, the battalion distributed more than one million gallons of water from 8 December 2021 to 12 March 2022.