The Samuel P. Ely was wood framed and built almost entirely of white oak. The Ely has transverse frames of double flitch oak, several heavy longitudinal keelsons on the centerline to form the backbone, and a double skin of inner and outer planking. Data has been obtained on the condition of the wreck from sports divers and divers for the U.S. Army Corps of Engineers dive team, through interviews, and video documentation. The wreck is estimated to be 70 percent complete, with about 30 feet of the stern demolished or buried in rip rap, and about 15 feet or 20 feet of the bow damaged. However, all of the structural components of the bow appear to be at the site. The damage to the stern resulted from the 1896 accident which caused the vessel's loss. The damage was compounded by repairs made to the breakwater. Damage to the bow does not appear to have resulted from simple structural weakness or deterioration, but rather from accidental strikes by vessels. This could be explained by anchor damage from working harbor maintenance craft, or from larger commercial ships.

The Ely's hull is still largely intact. Besides the broken bow and stern, about one-third of the deck planking is missing, giving the wreck a feeling of openness when seen from within. The sides and deck framing are complete, and much of the decking and hatch coaming is still in place. The damage to the stern consists of the outward displacement of both sides and the collapse of the decking into the hold, with large 2-foot to 6-foot rocks lying on top of the wreckage. The decking angles down into the rocks at a slope of about 30 degrees from the horizontal for a distance of about 20 feet, from which point it is intact for about 100 feet towards the bow. The bow is opened outward along the vertical axis of the stem, with the heavy stem and apron timbers lying to the starboard side. The port side is displaced farthest from its natural position, but both sides are splayed outward. The port side of the bow is crushed and fragmented as though it had been struck.

Under most circumstances the water conditions at the site of the Ely wreck are calm and protected, but cloudy. Visibility ranges from 2 feet to 10 feet most of the time depending on wind direction and velocity, groundwater run-off, and vessel traffic. The wreckage is covered with a thin layer of light silt. Any slight current, ship movement, or sports diving activity quickly generates a cloud of suspended particulate matter which is very slow to settle.

Least depth over the wreck is 12 feet to 15 feet, and there is reason to believe that portions of the railings and deck machinery projected a few feet higher in earlier times. The wreck is located in water with an average depth of 35 feet. It is on an even keel, with the stern in slightly deeper water. The bottom is fairly flat and muddy with a scattering of small rocks and debris and about a foot of loose, silty grey-brown clay. The orientation of the wreck is 30 degrees relative to the breakwater. The stern of the ship intersects the breakwater near its western end.