There are definitely many habitat problems on Hammersley Fork. Lots of very shallow water, lacking in pools and cover.
I don't think that is new. It was that way when I fished there 30 years ago.
The important questions are: 1) What are the causes? 2) What can be done to restore more normal stream/floodplain structure and processes?
From Route 144 up to the last cabin just below Beech Bottom, the main problem is the cabins in the floodplain and the access roads to them, as already described.
The stream in that long stretch is essentially a straight ditch, and has extremely poor habitat because of that. As long as the cabins are there, it will have to be managed as such, to protect the cabins. If the stream begins to meander and accumulate large woody debris and form channel splits and re-joinings, like a natural stream, that would threaten the cabins and dirt roads with increased flooding and channel avulsions.
In that area there has been a lot of manipulation of the stream, in order to keep it flowing in a simple path, to prevent it from destroying the cabins and access roads.
The effects of that propagate upstream. So even when you get above the last cabins, the stream is shredded.
But from the last cabin up to the headwaters, the main problem is the old logging railroad grade, which was built around the 1880s. And after the logging was done, the old grade was used as a woods road up until modern times. I'm not sure when it was really blocked off. But as I recall, in the late 1980s, there were signs at Beech Bottom saying no vehicles beyond this point, but many people still drove up past there. Then rocks were piled up to close it off. I'm not sure of the date, but I think it was roughly late 1980s. I remember seeing tire tracks way up, as late the late 1980s.
The old grade is in the floodplain in many places. In places the stream appears to have jumped into the old grade, which creates a simplified, ditch-like, straight-down type of channel, which produces terrible habitat.
The old grade has never been re-colonized by vegetation. So you don't get the influences of tree roots, leaning trees, and downed trees that normally produce pools and cover.
Also, during the logging days, probably the entire stream channel was altered to accommodate the railroad grade in the floodplain. The streams normal structure would be wandering from side to side across the floodplain, and with numerous channel splits and re-joinings.
Pools commonly form at bends and where channel splits rejoin. Normal stream structure would also includes large amounts of leaning and downed trees and logjams, which interact with the flowing water to form pools and cover.
But a normal, complex stream, highly connected to its floodplain and that undergoes changes in every major flood like that is incompatible with a having a railroad grade or road grade in the floodplain. So they simplified the stream. You see this not just in Hammersley, but everywhere in PA.
All of the original "woody debris" was surely removed when they built the logging railroad grade. And all of the large trees were logged off.
So, what would should be done for restoration? From the last cabin up to the headwaters, what should be done is to "rip" the old grade, i.e. dig up the compacted soil and reforest it by planting trees and shrubs. In any place where the grade is raised above the normal floodplain surface, and acts as a wall that blocks floodwater flows and prevents the stream channel from moving, it should be leveled out to the normal floodplain elevation, then plant trees.
The hiking trail up the valley should probably relocated in many places, to keep it well away from the stream. And it should be out of the floodplain as much as possible.
The main cause, IMHO, is the old logging railroad grade which was built around the 1880s, and which was then used as a woods road up until modern times.