Ship Service: How the Navy Was Built on a Flotilla Gunboats To serve as crewmembers on these early gunboats as well as on some of the newer models, the Department of the Navy ordered some five hundred seamen from eastern seaports to serve along the western waterways. Here’s What You Need to Remember: In theory, sealing off Southern seaports was supposed to cause economic ruin in the South, which in turn would diminish the Confederacy’s ability to wage war. However, gaining control of the Mississippi River was to have more of a direct impact on military strategy. If Union forces in the West were to penetrate into Confederate territory as planned, it was critical that they obtain control of the river. If the North could not, it would be forced to defend extended lines of land communication.