Anybody who has been to Harper's Ferry has seen the famous security building where John Brown and his men surrendered, and most visitors have noticed the monument marking the spot where that building originally stood, but the NPS doesn't do a particularly good job of explaining with their signs and diagrams how everything was originally oriented, how the layout impacted events of the raid, or what has changed over the years since then. I'm going to try to talk you through it. Getting all this in my head was not easy, and you may need to read through this twice, as the railroad has made quite a mess of things.
First of all, ground level has been elevated where the monument sits. The security building once sat there down at street level, with its back to the camera. Wagon and horse traffic would have been approaching from right to left, on the street behind the stop sign, and would have needed to make a square left turn in front of the security building to enter the arsenal's main complex and go down in between the two long rows of buildings, behind the camera from this point.
The Shenandoah River is directly in front of you, and the Potomac is to the left.
Now, let's look at the arsenal's main buildings.
The longest and most important manufacturing building is the one with the tall square chimney, which almost looks like it's part of the railroad bridge in the old faded picture. There's another low section of it hidden behind the two story building; the higher part with the chimney was in the middle. Note the elevated railroad track between the buildings and the water's edge, snugged up against a flood wall that you can't see. On the uphill side of the complex, not the narrow canal for water power. Water exited this canal in several places and entered pipes that took it through various buildings, where the water turned a shaft that powered all the larger machines in each building, before flowing into the river through two openings in the flood wall.
The footprint of the longest arsenal building is near the center of the picture above, where the grass is a little longer than the rest. We're now looking from the opposite end, with the Potomac on our right. The two story building's original footprint was mostly buried by fill dirt brought in for a railroad relocation. And the building closest to the camera in the old picture was about where the modern train station sits on a high fill, at the rear of the modern shot. Both openings in the flood wall for water power can be identified by the weeds that grow there.
This track actually lined up with the third generation of railroad bridge built on the site. Upper right, you can see a piece of the fourth generation bridge. Since the track in the foreground is no longer used, it could be removed, along with the fill dirt under it, restoring this part of the arsenal site to its original elevation, size, and shape. This includes the spot where the monument stands, meaning that the security building could be put back exactly where John Brown found it.
This stone support held up the first and second generation railroad bridges over the Potomac. You can see a change in stone color where the pier was modified to make the second (open) bridge higher than the first (covered). Two tracks converged here in 1860, and the junction switch was in between the first and second pier. Beyond this stonework, you can see the third and fourth bridges, both still in use. There was no tunnel in 1860. On the Maryland side, the track curved sharply to the right and went around the end of the mountain.
Below, seeing the relocated security building from the back, you can look to the left of the center of the picture and just barely see part of the monument marking its original location, partly hidden behind another building. Originally, it would have been pretty much in line with that building, facing the same way, and on the same level. All of the dirt above street level was brought in later.
If you're finding any of this at all confusing, let me make it worse by throwing in another twist. John Brown wasn't particularly interested in the main arsenal complex. He didn't want gun parts or machinery to make muskets. He wanted completed muskets that were ready to be used. Those were kept in two warehouse buildings. Those were the main objective of his raid. The footprint of the larger of the two warehouses is in the foreground above. The smaller one was beside it, behind the camera.
He would have also needed musket balls and black powder, which would have required some time spent in the main complex. I wonder if he studied the layout of the facility in advance and knew exactly where he needed to go, or if he was just planning on figuring it out when he got there. I haven't yet found a definitive answer to that question. He didn't get much time to look around.
Moving on a few years...
Near the security building and also one end of the longest arsenal building, this break in the flood wall and ramp down to river level was used as a boat landing. Early in the Civil War, the permanent bridge over the Potomac was destroyed, and a pontoon bridge was anchored at the bottom of this ramp. The distant railroad bridge is generation four, built much later.
Not much else original from the CW era survives in Harper's Ferry, not that there was a huge amount to begin with. It was a small town. The house below has been expanded several times. The oldest piece on the left is the original Harper house, where the owner of the ferry lived. It didn't take long for people to figure out that a bridge was needed here, as the Potomac water level tended to fluctuate between too low and too high for ferry operations. The house was expanded at least once while it was in the Harper family, then the US Army took it over and added significant barracks space in multiple projects. It was used in this role when the arsenal was active.
This hilltop church is also pre-CW: