Tracking Lagrangian coherent structures in dynamical systems is important for many applications such as oceanography and weather prediction. In this paper, we present a collaborative robotic control strategy designed to track stable and unstable manifolds. The technique does not require global information about the fluid dynamics, and is based on local sensing, prediction, and correction. The collaborative control strategy is implemented on a team of three robots to track coherent structures and manifolds on static flows as well as a noisy time-dependent model of a wind-driven double-gyre often seen in the ocean. We present simulation and experimental results and discuss theoretical guarantees of the collaborative tracking strategy.