As the others have said, if the stream is "navigable" the landowner can only own up to the bank and you can wade as long as you stay within the high water mark (this was the basis of the Little Juniata case). If it is not "navigable" the landowner also owns the stream bed, so you can not set foot on the stream bed if he doesn't want you to. Now, if the other side of the stream is open to the public, that brings up an interesting question. I believe that the landowner only owns to mid-stream, but maybe this could vary with the deed. The landowner doesn't own the water, so you should be able to fish from the public side. Another interesting issue is whether you could canoe through a non-navigable private stream without trespassing. I believe you can, although that then brings up the question as to whether the stream may be navigable, if you can easily float it for long distances.
Concerning Padraic's statement about rivers being officially declared navigable in court, I believe that if they meet the general characteristics of a navigable stream, they are considered navigable. They don't have to be declared navigable. This is only necessary if there is a dispute big enough that someone wants to take it to court. In the Little Juniata case the state told Beaver that it was their opinion that the stream was navigable and he should desist from claiming it as his own. He continued to dispute this, but I'm not sure who then eventually filed the court case.
The practical issue is whether the stream you want to fish is navigable. Although it may be arguable whether "small" creeks that you can canoe long distances are navigable, I wouldn't be getting into arguments with landowners along small creeks over the issue. Even for streams that are as big as the Little Juniata, if the landowner doesn't want you wading through, I would avoid it or check with the PFBC. Maybe they don't really have the right to keep you out, but they may think they do, and it may take a letter from the authorities or even a court case to settle it. But I wouldn't worry about wading the Dealware, Susquehanna, and Ohio rivers alongside private property (except in the small headwaters, but where does that line begin???!!!).