I really feel bad about removing any of these last ones from the list, so I'll cheat and group them by general topic area... in the groups like "general overviews," they mostly cover similar ground, for instance, though some have a different angle on it. My current "go-to" recommendation for those who only want to read one book is James M. McPherson's
War on the Waters, both because it's good and because it's recent and therefore widely available.
General Overviews
Anderson, Bern. By Sea and By River. New York: Alfred A. Knopf, 1962. 303 pp.
Fowler, William M. Under Two Flags: The American Navy in the Civil War. New York: Avon Books, 1990. 352 pp.
McPherson, James M. War on the Waters: The Union and Confederate Navies, 1861-1865. Chapel Hill, N.C.: Univ. of North Carolina Press, 2012. 267 pp.
Surdam, David G. Northern Naval Superiority and the Economics of the American Civil War. Columbia, S.C.: Univ. of South Carolina Press, 2001. 286 pp.
Tucker, Spencer C. Blue and Gray Navies: The Civil War Afloat. Annapolis: Naval Institute Press, 2006. 426 pp.
Tucker, Spencer C. Short History of the Civil War at Sea, A. Wilmington, Del.: SR Books, 2001. 188 pp.
West, Richard S., Jr. Mr. Lincoln's Navy. New York: Longmans, Green and Co., 1957. 328 pp.
The Blockade and Coastal Actions
Browning, Robert M., Jr. From Cape Charles to Cape Fear: The North Atlantic Blockading Squadron During the Civil War. Tuscaloosa, Ala.: Univ. of Alabama Press, 1993. 309 pp.
Browning, Robert M., Jr. Success Is All That Was Expected: The South Atlantic Blockading Squadron During the Civil War. Washington: Brassey's Inc., 2002. 359 pp.
Browning, Robert M., Jr. Lincoln's Trident: The West Gulf Blockading Squadron During the Civil War. Tuscaloosa, Ala.: Univ. of Alabama Press, 2014. 712 pp.
Buker, George E. Blockaders, Refugees, and Contrabands: Civil War on Florida's Gulf Coast, 1861-1865. Tuscaloosa, Ala.: Univ. of Alabama Press, 2004. 196 pp.
Davis, William C. Duel Between the First Ironclads. Garden City, N.Y.: Doubleday, 1975. 201 pp.
Fonvielle, Chris E., Jr. Wilmington Campaign, The: Last Rays of Departing Hope. Campbell, Calif.: Savas Publishing, 1997. 623 pp.
Friend, Jack. West Wind, Flood Tide: The Battle of Mobile Bay. Annapolis: Naval Institute Press, 2004. 336 pp.
Hearn, Chester G. Capture of New Orleans, The, 1862. Baton Rouge: Louisiana State Univ. Press, 1995. 292 pp.
Merrill, James M. Rebel Shore, The: The Story of Union Sea Power in the Civil War. Boston: Little, Brown, 1957. 246 pp.
Roberts, William H. Now for the Contest: Coastal and Oceanic Naval Operations in the Civil War. Lincoln, Nebraska: Univ. of Nebraska Press, 2004. 223 pp.
The Western Rivers
Cooling, Benjamin Franklin, III. Forts Henry and Donelson: The Key to the Confederate Heartland. Knoxville, Tenn.: Univ. of Tennessee Press, 1987. 354 pp.
Daniel, Larry J. and Bock, Lynn N. Island No. 10: Struggle for the Mississippi Valley. Tuscaloosa, Ala.: Univ. of Alabama Press, 1996. 216 pp.
McCaul, Edward B., Jr. To Retain Command of the Mississippi: The Civil War Naval Campaign for Memphis. Knoxville: Univ. of Tennessee, 2014. 239 pp.
Merrill, James M. Battle Flags South: Story of the Civil War Navies on Western Waters. Cranbury, N.J.: Fairleigh Dickinson Univ. Press, 1970. 334 pp.
Milligan, John D. Gunboats Down The Mississippi. Annapolis: US Naval Institute, 1965. 217 pp.
Shea, William L. and Winschel, Terrence L. Vicksburg Is the Key: The Struggle for the Mississippi River. Lincoln, Nebraska: Univ. of Nebraska Press, 2003. 242 pp.
The Navy and Command
Canney, Donald L. Lincoln's Navy: The Ships, Men and Organization, 1861-65. Annapolis: Naval Institute Press, 1998. 220 pp.
Symonds, Craig L. Lincoln and His Admirals. New York: Oxford Univ. Press, 2008. 256 pp.
Taaffe, Stephen R. Commanding Lincoln's Navy: Union Naval Leadership During the Civil War. Annapolis: Naval Institute Press, 2009. 324 pp.
Sailors' Experiences
Bennett, Michael J. Union Jacks: Yankee Sailors in the Civil War. Chapel Hill, N.C.: Univ. of North Carolina Press, 2004. 210 pp.
Grattan, John W. and Scheller, Robert J., Jr. Under the Blue Pennant: Or Notes of a Naval Officer, 1863-1865. New York: John Wiley & Sons, 1999. 239 pp.
Hill, Jim Dan and Stedman, Charles Ellery. Civil War Sketchbook of Charles Ellery Stedman, Surgeon, United States Navy, The: Biography and Commentary. San Rafael, Calif: Presidio Press, 1976. 213 pp.
Hunter, Alvah F. and Symonds, Craig L. (ed.) Year on a Monitor and the Destruction of Fort Sumter, A. Columbia, S.C.: Univ. of South Carolina Press, 1987. 208 pp.
Lamson, Roswell Hawks and James M. McPherson, Patricia R. McPherson. Lamson of the Gettysburg: The Civil War Letters of Lieutenant Roswell H. Lamson, US Navy. New York: Oxford Univ. Press, 1997. 240 pp.
Marvel, William. Alabama and the Kearsarge, The: The Sailor's Civil War. Chapel Hill, N.C.: Univ. of North Carolina Press, 1996. 348 pp.
Marvel, William (ed.). Monitor Chronicles, The: One Sailor's Account; Today's Campaign to Recover the Civil War Wreck. New York: Simon & Schuster, 2000. 272 pp.
Ramold, Steven J. Slaves, Sailors, Citizens: African Americans in the Union Navy. DeKalb, Ill.: Northern Illinois Univ. Press, 2001. 262 pp.
Ringle, Dennis J. Life in Mr. Lincoln's Navy. Annapolis: Naval Institute Press, 1998. 202 pp.
Thomsen, Brian M. Blue & Gray at Sea: Naval Memoirs of the Civil War. New York: Forge Books, 2003. 445 pp.