Due to the reputation of the Chicago Light Guard, Marsh was called to Springfield, Illinois at the outset of the Civil War.

Colonel Marsh and the 20th were stationed at Bird's Point, Missouri until joining Ulysses S. Grant's expedition to Fort Henry as a part of W. H. L. Wallace's 2nd Brigade in John A. McClernand's 1st Division.

Despite being hard pressed Marsh managed a counterattack which momentarily checked Simon B. Buckner's division and saved an Illinois artillery battery from capture.

[5] Following the victory at Fort Donelson, General Ulysses S. Grant was thrust into the public eye and at the same came under attack from department commander Henry W. Halleck.

[7] Early in the fighting Marsh's brigade was forced into a disorderly retreat until he and General McClernand managed to rally units of the 1st Division behind Shiloh Church.

He was transferred to command the 1st Brigade in John A. Logan's 3rd Division of the XVII Corps in the opening stages of Grant's First Vicksburg Campaign.