The site of the Appomattox lies in 15 to 20 feet of water, approximately 150 yards off Atwater Beach in the village of Shorewood, Milwaukee County. The Wisconsin Historical Society places a mooring buoy on the site during dive season. A 250-foot section of the Appomattox’s lower bilge remains intact, with her bow facing southwest. A 260-foot section of the port hull lies adjacent to the wreck, having collapsed and fallen away from the lower bilge section. The ship’s boilers and engine were salvaged, but remnants of the engine beds remain. A large four-bladed propeller, which lies approximately 500 yards southeast of the site, probably belongs to the Appomattox.

The propeller lies approximately 500 yards southeast of the wreck

A small debris field lies north and east of the bilge section. It includes remnants of steam pipes, iron plates and miscellaneous associated items. Little of the coal cargo remains. Some was lightered in attempts to pull the Appomattox free, and the remainder washed ashore over several years and was collected by Milwaukee residents. Off the stern is a large wooden timber, probably remains of the sternpost and associated deadwood.

The keelson was reinforced on each side with iron plates (bending in foreground)

The timbers and scantlings are remarkably large, as would be expected on the world's largest wooden ship. The vessel's major longitudinals include a main keelson , with multiple floor keelsons set on either side. In the midships area, additional floor keelsons are placed at the turn of the bilge. Two wooden stringers run along the top outermost edges of the center keelson, where the deck stanchions were once fastened. On either side of the main keelson are six floor keelsons. Transverse spacers separate the main keelson and the first floor keelson. Several limberboards remain atop the keelson spacers. Floor keelsons were a common addition to large wooden vessels, running the full length of the vessel and providing longitudinal strength to prevent sagging and hogging of the vessel ends.