I was recently fishing some small water with little flow. While it can run pretty shallow and clear, it holds a decent amount of fish and can be a pretty popular spot. Because of the flow and the pressure, being stealthy can significantly up your chances. The fish get line shy and even by this point of the season are lightly taking flies. I was surprised when a guy a little downstream was chucking a bright pink extra large ( 11/4) Thingamabobber.
Running an over-sized indicator increases the chances of spooking fish, makes it harder to detect subtle takes, can complicate casting (especially in wind) and gives you difficulty feeling the streams bottom.
Downsize your indicator to something that is just big enough to float.