A collaborative control method for tracking Lagrangian coherent structures (LCSs) and manifolds on flows employs at least three autonomous underwater vehicles (AUVs) each equipped with a local flow sensor. A first flow sensor is a tracking sensor and the other sensors are herding sensors for controlling and determining the actions of the tracking sensor. The AUVs are deployed in a body of water whereby the tracking sensor is positioned with respect to the herding sensors such that the herding sensors maintain a straddle formation across a boundary. A local flow velocity measurement is obtained from each AUV; and based on the local flow velocity measurements a global flow structure that is useful for plotting an optimal course for a vessel between two or more locations is predicted.