OK, I think I know what the problem is now. you said that you drew the rivers in with the "Pencil" tool. Unless I'm mistaken here, you need to draw the river outlines using the "Paths" tool. This means that you will have several individual river paths (for each river, or segment of a river that you want to taper at a different width). You then apply the tapered stroke path to each of these paths (making sure that your rivers layer is selected). Hope that helps.

Cheers,
-Arsheesh