When I was taking pictures by a local creek, I moved into place to take my shot and noticed that when I stoppped the Spark would drift back. I belive it was using the bottom sensor to lock onto. The water was moving backwards making the spark drift back with it. What I am worried about is that the Spark may drift back into a branch. Is there a way to avoid this?

You can raise the spark to a higher altitude so the sensors don't get confused, or you can just manually correct the position with your RC sticks.

I agreed with viking. Please cross the water in a higher altitude when you fly your spark.  Or it will affect the 3D vision sensor.