The southern end of an 1861 Confederate earthwork was excavated from 2003 to 2008 in order to investigate the features from James Fort below. During the course of the excavation, multiple features associated with the earthwork were uncovered. The most expansive of these was the gun platform for the fort's canon. This platform stretched for 158 feet from east to west and averaged 16 feet wide. The surviving evidence for this platform consisted of the entrenched joists, large iron spikes, and wood remnants that had held the platform together. Nearly 100 joists were found along with almost 1000 spikes. A ramp leading to this platform was also identified. The remains of the platform were carefully mapped, photographed, and recorded by the archaeologists.
In addition to the gun platform, three large powder magazines from the 1861 fort were identified. All three of these powder magazines were partially excavated. One was brick lined and circular and contained a collapsed burned wooden roof. The Union cavalry inspecting the fort in May 1862 after its abandonment by the retreated Confederate army recorded that "the battery was abandoned, the magazines and gun carriages were burned." Another larger powder magazine, nicknamed the bombproof, was found disturbing the western palisade of the 1607 fort. The bombproof was large and two air ventilation shafts were found leading into the collapsed interior chambers of this structure. Excavations stopped short of exploring the room or rooms associated with the bombproof. A third smaller powder magazine was located due west of the bombproof.
Several other notable features from the Civil War period included a hearth with charred timber remains carved into the earthwork, remnants of a wooden walkway, and a curious "saw tooth" shaped ditch. Only a handful of artifacts relating to the Civil War period were found during the excavations of the earthworks. Numerous James Fort period artifacts were recovered in earthwork fill, being redeposited from fort period features. The northern half of the Confederate earthwork remains intact and is outside the bounds of James Fort.