@KianGaf and
@Rusk County Avengers -- I compared this structure with the 1891 US War Dept map of the Charleston defenses, and, as I thought, this location on the north of James Island seems to have been submerged at the time of the Civil War. I think the coastline around the harbor has changed considerably over the years -- for example, Morris Island has eroded quite a bit, threatening the sites of Batteries Wagner and Gregg.
Here's a Google sat map showing that structure close to the center of the triangle of Forts Johnson and Sumter and Battery Simkins:
View attachment 367020
And here's a detail from the 1891 War Dept map, which indicates that that location was under water at the time of the war. (By the way, the War Dept map was not oriented north-to-south in the customary manner, so I rotated it to orient to the Google map.)
View attachment 367021
That square also seems like an unlikely shape for a fort, but I don't know everything about fortifications. I'm wondering whether there are some Charleston experts here at CivilWarTalk that might be able to chime in.
@NFB22 might have an opinion also, or know someone familiar with the area. He put together a nice thread on Fort Johnson a while back:
Roy B.