Benjamin Sands was promoted to captain in 1862 and went to the North Atlantic Blockading Squadron where he commanded the USS Dacotah. In February 1863, he was involved in an engagement off Fort Caswell, guarding the port of Wilmington, North Carolina.
For the next two years he was stationed off the Carolina coast. While commanding the USS Fort Jackson, he participated in both battles of Fort Fisher.
In February 1865, he was transferred to the West Gulf Blockading Squadron and saw duty off the Texas coast. On June 2, 1865, he took formal possession of Galveston, Texas.