She assigned by the Union Navy during the blockade of ports and waterways of the Confederate States of America to a number of duties: as a tugboat, a dispatch boat, a troopship, and as an ammunition ship, mostly on the Mississippi River and its tributaries.

In returning down stream, Muscle sprang a leak and sank; but Sallie Wood descended safely and was taken into the Western Flotilla for service as a transport, a tugboat, and an ammunition ship.

While steaming along the navigable branches of the Mississippi River, Sallie Wood occasionally braved fire from masked riverside batteries.

In July, as she ascended the Mississippi carrying sick soldiers, she was fired upon by Confederate cannon concealed ashore at Carolina Landing, at Princeton, and at other points above.

Her pilot used the current to run her aground on the island, but the cannonade continued until all of the side wheeler's officers, crew, and passengers had been forced to leave the ship.