I have no idea of your specific situation, but I believe I read somewhere about some fellow who tried to do something like this on a stream going through his very own property (both sides) and got into some big trouble with the feds. Something about all navigable waterways being public, and the definition of navigable is pretty extreme. Even if the river, stream or creek dries up for most of the year, and can only handle as little as a canoe during short periods of the year, it's still considered navigable and as a result, the beds and banks are public, and any disruption of the flow by ajointing private owners without approval and permit risks serious fines plus restoration costs. The Army Corps of Engineers I think got involved with that case, and gosh the guy pretty much lost his life savings.
The bottom line was, you need to get approval from the appropriate authorities before messing with building anything effecting waterways, even if it's a tiny creek. It's not worth the risk of making an innocent mistake.