A collaborative control method for tracking Lagrangian coherent structures (LCSs) and manifolds on flows employs at least three autonomous sensors each equipped with a local flow sensor for sensing flow in a designated fluid medium, e.g. water or air. A first flow sensor is a tracking sensor while the other sensors are herding sensors for controlling and determining the actions of the tracking sensor. The tracking sensor is positioned with respect to the herding sensors in the fluid medium such that the herding sensors maintain a straddle formation across a boundary; obtaining a local fluid flow velocity measurement from each sensor. A global fluid flow structure is predicted based on the local flow velocity measurements. In a water medium, mobile autonomous underwater flow sensors may be deployed with each tethered to a watersurface craft.