The museum's centerpiece is the hull of C.S.S. Jackson, also known as C.S.S. Muscogee, a Confederate ironclad warship ram that never saw proper combat. Union troops under General James H. Wilson set her ablaze in the Chattahoochee River at the war's end. The burned-out hulk sank into the muddy riverbed, where it lay undisturbed for nearly a century before being recovered in the 1960s. Alongside Jackson sits what remains of C.S.S. Chattahoochee, another Confederate gunboat. Both vessels were listed on the National Register of Historic Places in 1970 when the museum was still known as the Confederate Naval Museum. The Georgia Historical Association praised the original museum building, designed by Columbus architects Biggers, Scarbrough and Neal, as 'an imaginative and quite contemporary canopy for the salvaged gunboats.'

The museum opened in 1962 as the James W. Woodruff, Jr., Confederate Naval Museum, named for the patron whose financial support made it possible. For decades it told only one side of the naval war. That changed in March 2001, when the museum relocated to a new eight-million-dollar facility at 1002 Victory Drive and took a new name: the National Civil War Naval Museum. The expanded collection now tells the story of both navies. Visitors can see an intact rowboat from U.S.S. Hartford, the flagship of Admiral David Farragut at the Battle of Mobile Bay in 1864. Full-scale sections of Farragut's ship are on display, including the berth deck, wardroom, and captain's cabin. Models of U.S.S. Monitor and C.S.S. Virginia, used in TNT's 1991 film Ironclads, sit alongside hundreds of authentic Civil War artifacts.

The museum holds the largest collection of surviving Brooke rifled naval cannons, massive weapons forged in Confederate iron foundries at Selma, Alabama. Four Brooke guns are on display: two 7-inch rifles, one 10-inch smoothbore, and an 11-inch smoothbore, the largest surviving piece of Brooke artillery. The flag exhibit, titled 'Ramparts to Topmast: Flags of Triumph and Despair,' is the largest display of Civil War-era naval flags in the nation. Fourteen flags representing ships and forts from across the entire conflict hang in the gallery. Among them is the C.S.S. Arkansas flag that Skelton stole, its fabric still bearing the wear of war and the century-plus of quiet storage in Ohio.

In 2009, the museum constructed a full-scale reproduction of U.S.S. Water Witch using original plan drawings. The replica became a Columbus landmark before deteriorating beyond repair and being demolished in October 2019. The original Water Witch had a story worth preserving. She was a Union blockade vessel stationed outside Savannah, Georgia, until a Confederate commando raid captured her in 1864. The raiding party was led in part by Moses Dallas, an African-American Confederate pilot. The Water Witch thus holds the rare distinction of having served under both flags during the war. The museum also features a battle experience theater that places visitors in the middle of a Civil War naval engagement, and an interactive ironclad ship simulator offering a taste of 19th-century combat at sea.