In November of 1861 USS New Era took part in an expedition up the Cumberland River.
Shortly thereafter she was renamed USS Essex and received an upgrade to iron armor and various other alterations.
On 11 January 1862 USS Essex engaged Confederate States Navy gunboats near Lucas Bend, Missouri. On 6 February 1861 she took part in the attack on Fort Henry, Tennessee and was badly damaged by Confederate gunfire.
Commanding officer William D. Porter upgraded his ship without official authorization into an ironclad gunboat. Under his orders she was lengthened, widened, completely reengineered, and her appearance was changed drastically. New, more powerful, engines were put in place and she was rearmored.
After her upgrade Essex took part in operations near Vicksburg, Mississippi. On 15 July 1862 USS Essex was engaged with CSS Arkansas as that ship successfully ran past the Union fleets in front of the city. On 23 July Essex unsuccessfully attacked the Arkansas at her moorings but was repelled by the Arkansas and the shore guns under whose protection the Arkansas lay. Federal forces withdrew from Vicksburg shortly thereafter.
After withdrawing, Essex joined Admiral David Farragut's squadron and was the only Federal ironclad on the lower Mississippi River. On 5 August 1862 Essex helped repel a Confederate Army attack on Baton Rouge, Louisiana.
As Essex approached the steering mechanism of the Arkansas jammed and her crew was forced to scuttle her due to the presence of the Essex.
She was involved in the bombardment of Port Hudson, Louisiana and assisted during the occupation of Baton Rouge.
In May-July of 1863 she participated in the siege and capture of Port Hudson.
USS Essex took part in the Red River Campaign of March-May of 1864.
New Era was scrapped in 1870.
USS Essex has the reputation as one of the most powerful and effective gunboats on the Mississippi River.