It then fitted her out as a "tinclad" gunboat and commissioned her on 30 August 1864 for service on the Mississippi River between Columbus, Kentucky, and Memphis, Tennessee.

However, before she could proceed downstream to her station, she was ordered, on 23 September, to Cape Girardeau, Missouri, to guard that area against a reportedly imminent attack by Confederate troops under Brigadier General Joseph O. Shelby.

On 14 February, Siren was ordered to proceed to New Orleans, Louisiana, for temporary duty with the West Gulf Blockading Squadron during mop-up operations in Mobile Bay.

However, upon her inspection at New Orleans, it was decided that she would require such "extensive repairs, alterations, and adjustments" before she would be ready for service at sea, that she was promptly returned to the Mississippi Squadron.

Among her varied duties during the first months after the Confederacy collapsed, was the task of accepting the surrender of Southern troops and of disarming the region.