His daring runs of two different ram ships past the batteries at Vicksburg as well as operations on the Yazoo River won him praise from William T. Sherman and David Dixon Porter.
During the engagement, the Queen of the West rammed Arkansas but inflicted only minor damage and rejoined the Mississippi River Squadron ships above Vicksburg.
[7] In August, the USS Benton along with Ellet's rams Monarch and Lancaster, captured the CSS Fairplay at Milliken's Bend on the Mississippi River.
Ellet and the Queen of the West also conducted operations in the Yazoo River clearing mines and engaging Confederate batteries.
While the mission planned for December 31 was scrapped due to heavy fog, Admiral David Dixon Porter praised Ellet in a report to Secretary of War Edwin M. Stanton.
Major General William T. Sherman described Ellet as "full of energy and resources" in his preparations to run two of his rams past Vicksburg.
[5] Ellet intended to "run the gauntlet" of Vicksburg by cover of night, however delays resulted in passage of the guns at daybreak.
[12] Once past the batteries, Ellet's orders were to intercept Confederate boat traffic at the mouth of the Red River and specifically destroy the CSS City of Vicksburg.
Ellet found the City of Vicksburg docked, rammed her and set her ablaze with turpentine soaked balls fired from the guns of the Queen of the West.
[15] The barge went unnoticed by the Confederate forces and floated downriver ten miles (16 km) before being intercepted by the Queen of the West.
[16] The Queen of the West rendezvoused with the De Soto and on February 12, Ellet directed both ships down the Atchafalaya River to Simmesport, Louisiana, in search of Confederate forces.
[17] On February 14, Ellet led the Queen of the West and De Soto up the Red River and captured the steamboat Era No.
She came under heavy fire by the shore batteries of Fort DeRussy and was run aground onto the right bank by her pilot instead of backing down river as ordered.
[19] The De Soto was set ablaze to prevent her capture by Confederate forces and Ellet and crew escaped on the Era No.
Porter wrote in his report, "Had the commander of the Queen of the West waited patiently, he would, in less than twenty-four hours, have been joined by the Indianola...This is a serious disappointment to us [above Vicksburg], as we calculated certainly on starving on the garrison at Port Hudson by merely blockading the mouth of the Red River.
"[20] Porter also questioned whether Ellet and his crew abandoned the Queen of the West too easily since it was entered back into service by Confederate forces so quickly.
Both ships received heavy fire from the batteries and the Lancaster was run aground and sunk to avoid capture by the Confederate forces.
The Switzerland was damaged but was repaired and continued duty on the Mississippi until Vicksburg and Port Hudson were captured by Union forces.
[23] Ellet also commanded the infantry of the Mississippi Marine Brigade until he requested a leave of absence due to poor health.