He served in the steam frigate Roanoke during the early months of the Civil War and later in 1861 was assigned to work with John Ericsson on the construction of the ironclad turret ship Monitor.

Much of the success of these two operations was due to his inspired work, and Chief Engineer Stimers continued an intimate association with the Navy's ironclad shipbuilding program for much of the rest of the Civil War.

He accompanied these ships during early operations against the Confederacy, most notably the 7 April 1863 bombardment of Fort Sumter, in Charleston Harbor, South Carolina, and helped repair them after that action.

Later in the year he was placed in charge of an ambitious project to construct twenty light-draft monitors for use in shallow inland waters.

Stimers had inadvertently demonstrated the inherent difficulty of successfully shepherding complex technological endeavors, something that has bedeviled "project managers" from his time to ours.