Again, the whole "I'm not an attorney" disclaimer applies.
In Colorado you cannot make any in-stream diversions (i.e. moving rocks, even by hand) without the permission of the USACE. They require drawings and calculations stamped by a professional engineer providing sufficient proof that there will be no change in the floodplain in the area as a result of your modifications. I believe this applies even if you own the adjacent property and for even the most minor of changes.
The reason for this is that you could increase the floodplain causing increased damage to properties outside of yours. Additionally, you could make small streambed changes to illegally take water from the stream.
Again, I'm not a lawyer but this is the way that I understood the water law when I researched it.
"The world would be a better place if everyone kayaked."-Brad Ludden (Valhalla)
"You only get one chance to run a drop blind."-DD