I just finished War on the Waters by McPherson. It is a short history of two navies in the Civil War. It is a good overall narrative of the war on the salt and fresh water and does a good job of showing how important those operations were to the overall war effort, especially the huge and critically important contribution the Union Navy made to the defeat of the CSA.

One thing of interest from the small war point of view is the problem the Federal forces had in protecting their river supply lines from Confederate irregular forces. The rivers could be considered the MSRs of their day-MSR Tennessee and MSR Cumberland so to speak-and the steamers plying them were subject to attack via field artillery and small arms from the shore. What the Union Navy did was to arm and armor (lightly armored , hence 'tinclads') other river steamers and use them for convoy escort and patrol. An example tactic cited was a column of cargo steamers on its way with a number of tinclads interspersed. That sounds familiar.

http://www.amazon.com/War-Waters-Con.../dp/B0093A42XY