Wyandotte was on militia duty when the Spanish–American War began and she was recommissioned in 1898 to defend Boston, Massachusetts from any Spanish raiders.

A "rifle screen" of 1⁄2-inch (13 mm) armor 3 feet (0.9 m) high was installed on the top of the turret to protected the crew against Confederate snipers based on a suggestion by Commander Tunis A. M. Craven, captain of her sister ship Tecumseh.

[10] Completion of the ship was further delayed by the low depth of the Ohio River which prevented her movement from Cincinnati in December 1864 to finish their fitting out.

Wyandotte was moved to Evansville, Indiana in late May to complete her hull where rudimentary facilities and illness among her workers delayed her construction still further.

[11] The monitor joined her sisters Oneota, Manayunk, and Catawba[12] in ordinary[8] opposite Cairo, Illinois[12] when she was completed on 15 February 1866[2] although they drew enough water that they had to be anchored in the main channel where they were often struck by debris, drifting ice, and were vulnerable to accidents.

In 1873–74, Wyandotte was thoroughly overhauled by John Roach & Sons in Chester, Pennsylvania and commissioned for the first time on 24 January 1876, under the command of Lieutenant Thomas C. Terrell.

The ship was assigned to the North Atlantic Squadron through 1879 and spent her time on exercises and training cruises; she was based at Hampton Roads, Virginia for a while.

[8] Wyandotte was transferred to the Connecticut Naval Militia in 1896, and she was recommissioned for local defense duties on 30 April 1898 during the Spanish–American War in response to political pressure.