I've been doing a lot of poking around about Mound City, as Walke (of course) was the station commander after the war, during what was effectively the draw-down and demobilization of the Mississippi Squadron's infrastructure (most of the gunboats were gone already, but there was still a lot around to deal with... Mound City had gone from nothing to the Navy's second or third largest shore installation in just a few years).
The first photo is looking down-river, towards the southwest. The building in the distance (cross-wise to the view) was the sawmill; just beyond the sawmill but not visible are the marine ways, basically a number of rails almost like railroad tracks (but many of them, in parallel), with a couple of cradles that ran on them that were drawn up and down the rails by a powerful steam engine to haul boats out of the water for maintenance. The building closer to the camera is a machine shop, with a blacksmith shop just on the right side of the photo.
The tinclad in the foreground has been identified as USS Tensas, but the unfortunate placement of the bell makes this not 100% certain (is that a zero or a nine behind it?). Astern/downstream of her is an unpowered barge of some sort, probably more repair facilities; and there's some sort of scow or barge in the river between the Tensas and the bank. The photo was taken from the deck of another vessel tied up upstream of the Tensas.
The second photo is looking generally upstream, in a northerly direction (the Ohio River flows just about northeast to southwest where Mound City is located). The building on the far right is either offices or a gun carriage storage building (two maps disagree on this particular building [but it looks more like offices to me]). The small roofed-over structure that looks like a picnic pavilion is about where the maps say there should be a defensive battery. The most prominent building, with a sort of framework tower at one end, is the ordnance office. Immediately to the left of the ordnance office, you can see "The Mound," a portion of the levee protecting Mound City from the Mississippi; this might have been a pre-existing Indian burial mound (one of those that gave Mound City its name) that was incorporated into the levee system. The track-like structures set into the bank, I'm not 100% sure about; I know it's not the marine railway system, as that's located a few hundred yards downstream. The photo is possibly taken from the same vessel as the first photo, though of course in a different direction.
(The buildings or houses just visible on the right side of the second photo are beyond the naval station and are part of Mound City proper. A little farther to the right would be the Hospital; too bad the photographer didn't include it in the image.)