On the 17th, Sachem was assigned to the United States Coast Survey and, with the assistant in charge, soon sailed for the Gulf of Mexico where Flag Officer Farragut was preparing to attack New Orleans.

Sachem entered the Mississippi on 12 April; and, "...while exposed to fire from shot and shell, and from sharpshooters in the bushes," her boats surveyed the river from the passes to positions just below forts St. Philip and Jackson.

But the triangulation continued; and, when Farragut moved his fleet up the river on the 15th, charts prepared by the Coast Survey guided each of Porter's vessels to a position from which it could fire accurately at one of the forts while suffering minimum exposure to enemy guns.

In the days that followed, whenever a vessel changed its position, an officer of the Coast Survey would immediately calculate the new distance for her gunners, enabling them to resume their extremely accurate fire.

Sachem, after supporting Farragut near New Orleans, arrived at Ship Island, Mississippi on 5 May, but got underway later that day to reconnoiter Lake Pontchartrain and the Pearl River.

On the 8th, when the steamer USS Clifton ran aground on Southeast Shoal under the guns of Fort Morgan, Sachem, ignoring the Confederate fire, steamed in to help refloat the ship.

The appearance of the Union warships off Mobile Bay prompted Confederate forces to destroy and evacuate the navy yard at nearby Pensacola, Florida.

Porter assisted Brigadier General Lewis G. Arnold in occupying and restoring the abandoned works which soon became a valuable Union naval base in the gulf.

On 16 May, while writing to the Superintendent of the Coast Survey, Porter mentioned Sachem leading three steamers up the Pearl River seeking Confederate gunboats reported there.

Once past the Confederate batteries at Port Hudson, he intended to blockade the mouth of the Red River to stop the flow of men and supplies from the west to Southern armies fighting east of the Mississippi.

That afternoon, as the mortars began a slow bombardment of the lower riverside breastworks, Sachem steamed up close to Southern batteries tempting them to reveal the positions of their cannon; but the Confederate guns spurned the bait and remained hidden.

As darkness fell, Farragut moved his assault forces, three steam sloops-of-war—each lashed to a gunboat—and side-wheeler, USS Mississippi, up to predetermined positions just out of range of Port Hudson's artillery.

After supporting Farragut's attack on Port Hudson, Sachem was based at Baton Rouge, to help maintain Union control of the lower river.

In April, while proceeding to Berwick Bay, La., to replace USS Diana which had been captured there on 28 March, Sachem developed serious leaks which forced her to return to New Orleans.

When Porter daringly raced his gunboats down the Mississippi past the batteries at Vicksburg, Admiral Farragut decided to leave the river and turn his attention back to the blockade of the gulf coast.

On the morning of 8 May, he left his flagship, Hartford, and embarked on Sachem for passage back down the Atchafalaya to Brashear City, La., where he boarded a train for New Orleans.

Sachem then returned by the back route to the Mississippi between Vicksburg and Port Hudson where she served as a dispatch vessel carrying messages and supplies between Army and Navy units besieging those two Southern river strongholds.

Early in July, the fall of those fortresses opened the entire Mississippi to Union shipping and freed Sachem for duty in the Berwick Bay–Atchafalaya area which occupied the gunboat during the summer.

Early in September, Sachem was assigned to a joint Army-Navy expeditionary force mounted at New Orleans to attack Sabine Pass, Texas.

Arizona and Granite City then began to withdraw; so Lt. Johnson, with no possibility of saving his ship, ordered her Parrott gun spiked; her magazine flooded; and her signal book and spy glass destroyed.