I dont know that the tribs are comparable to the main river however, especially the portion of the susqy from the confluence of it and the Juniata above Harrisburg.
They flow through drastically different areas with different problems encountered on each. The Juniata is a mainly rural flowing river with few occurrences in concrete jungles and the Susqy (again referencing below the confluence) flows considerably urban. The J river deals with pasture runoff, granted, but I have to imagine the salt and road waste from 322 and I-81 coupled with the crap that ends up in the river from Harrisburg has to be more damaging to the Susqy.
Another consideration, how much water is taken from the Susquehanna and used by communities along it's banks? That's gotta be considered as part of the low water problem as well, right?
I'm not a scientist, just kinda throwing stuff out there that makes sense to me. I may be way off base, but I believe these to be valid points.