Guess I'll throw in my opinion again... Rocks in the bottom: no! Rocks in a river: yes!
And here's why: As mentioned above, the rocks in the bottom of a pond collect gunk, and it's near impossible to get it cleaned out without moving all the rocks. On the other hand, in a shallow, fast-moving stream the water is continually stirred, even down between the rocks, so very little gunk has a chance to accumulate. I have pea gravel in my stream, but I think a little larger rock would have been better. The pea gravel is small enough to trap pockets of gunk, so I make a point of stirring it up at least every Spring. At least with the shallow water, the rock is easy to get to, but I might try switching it out for some 1" river rock at some point -- both because it will trap less waste, and because it will probably stay in place better and not try to wash downstream.