In March 1862, Waddell was appointed a Lieutenant in the Confederate States Navy. Sent to New Orleans, he was assigned to the incomplete ironclad CSS "Mississippi" until her destruction in late April. The next month, while serving as an artillery officer ashore, he participated in the battle between Confederate shore batteries and Federal ironclads at Drewry's Bluff, Virginia. He saw more shore-battery service at Charleston, South Carolina, during the rest of 1862 and into 1863. Sent abroad in March 1863, First Lieutenant Waddell was stationed in England awaiting the availability of a seagoing position.