In a few of the descriptions for Water Pulse, it notes that Water Pulse is a move where the user fires ultrasonic waves at the target. You know how bats use echolocation to find where they are? Well think of it like the user is shooting those bat noises all over the target, and the target, being a Pokemon has very good hearing, becomes disoriented by these noises and becomes confused. I hope that wasn't too hard to follow :)