In August 1863, the regiment was converted to mounted infantry for the remainder of the war.
The 16th Indiana Infantry was organized at Indianapolis, Indiana and initially served on a one-year enlistment from May 27, 1861, through August 19, 1862, and mustered again on August 19, 1862, for three years' service under the command of Colonel Thomas J. Lucas.
The regiment was attached to Manson's Brigade, Army of Kentucky.
Captured and reorganized after the battle of Richmond, it was attached to 1st Brigade, 10th Division, Right Wing, XIII Corps, Department of the Tennessee, to December 1862.
1st Brigade, 1st Division, Sherman's Yazoo Expedition to January 1863.
1st Brigade, 10th Division, XIII Corps, Army of the Tennessee, to July 1863.
1st Brigade, Cavalry Division, Department of the Gulf, to June 1864.
4th Brigade, Cavalry Division, Department of the Gulf, to August 1864.
Assault and capture of Fort Hindman, Arkansas Post, January 10–11.
Expedition to Greenville, Mississippi, and Cypress Bend, Arkansas, February 14–29.
Movement on Bruinsburg, Mississippi, and turning Grand Gulf April 25–30.
Regiment mounted and assigned to duty along eastern shore of the Mississippi, protecting transportation to New Orleans and points along the coast until October.
Bayou de Paul Carroll's Mills April 8.
Ordered to report to General Cameron, and assigned to frontier and patrol duty in District of Lafourche, Department of the Gulf, until June 1865.
Expedition from Terre Bonne to Bayou Grand Caillou November 19–27.
Expedition from Morganza to Morgan's Ferry, Archafalaya River, December 13–14.
Expedition to Grand Glaze and Bayou Goula February 14–18 (Companies B, F, & K).