If the legs were actually in the water, then yeah, I'd suspect shake going on there, too.
Do you use Live View when doing these shots? Turning that on, and using the 10x magnification to see your focus is a real help. You can even use AF (at least, on the 40D and 7D) when you're "zoomed" in that way to get focused at a very, specific spot.
Depending on what you're trying to show, you may not want focus through the *whole* image; but you definitely want some subject for the eye to land on, that's in focus. Here, it could be the whole stream, or it could be just the band of rocks in the foreground. I think that the shot was fine, aside from the softness from, what I think is likely the correct culprit, vibration from the water against the tripod.
If you haven't checked it out yet, you should look at DoF Master
; you can play with their online tool at home, or download their iOS/Android app for "on the go". It's really quite handy to check out what your DoF is likely to be like in a given scenario.