Todd,
Unfortunately, your understanding of land/water ownership here in PA is not correct. I wish it was. I'm not a lawyer (thankfully), but laws concerning public rights to access on PA's waterways are quite murky, and only the courts seem able to resolve things (with considerable difficulty).
Unless a stream or river has been ruled "navigable," a landowner who owns property on both sides of a stream or river can post it and exclude anglers. Whether they actually "own" the land under the water is another question, but unless that is contested on grounds of navigability, they can pretty much do what they want. There is no list of navigable waters because navigability is not as simple as it sounds. It really has little to do with providing passage for boats.
Some of this traces back to "Crown" grants before the US was the US, but mostly it has to do with established historical patterns of commerce and travel. If it can be shown that a river or stream was historically and consistently used as a route of travel, commerce, and industry, then navigability may be established. But this happens on a case-by-case, piecemeal basis. On some major waterways, like the Susquehanna and Delaware, the status is pretty obvious to all concerned. On many smaller waterways, a landowner can get away with posting until someone contests it in court and is granted a favorable ruling.
Two trout streams that were posted by private clubs have recently brought this issue to the forefront here in PA. The first didn't receive nearly as much attention as the second. Posting by the Lehigh Flyfishers on the Lehigh River below Stoddartsville Falls in the Poconos was the first big contest. The court ruled that historical use, particularly by the lumber industry, established a navigable status for that river. Stoddartsville Falls is more than twenty feet high and requires a portage by any sane boater, so note again that legal navigability has little to do with clear passage.
The second and more recent ruling concerning the Little J and the infamous Mr. B drew a lot more attention. The pattern of historical commercial use on the Little J was very well established by the plaintiff's lawyers and experts, even though expert testimony for the other side tried to show that the river could only be used for commercial travel during periods of high water.
There are probably many other posted waters where navigability could be established by law, but all of this takes a serious commitment of time and money to resolve. When we are not complaining, most of us are busy trying to squeeze in a little fishing, and we can't do much about it. Really, establishing mutually respectful relationships between landowners and anglers could alleviate much of the problem, but the kind of "relationships" Mr. B's money can buy are hard to beat with courteous behavior. Petty greed coupled with the promise of instant gratification is a ruinous thing these days, and everyone seems to be grabbing as much as they can get.
Thanks for the kind invitation to share your precious peace and quiet. Sounds very nice, indeed.
Best,
Lloyd