Wake is the hydrodynamic footprint of a vessel at sea. The Earth’s magnetic field makes these footprints visible using magnetic sensors. Magnetic wakes induced by the motion of vessels may extend several kilometers and stay up long hours under certain conditions. From remote sensing point of view, in this work physical properties of this magnetic pattern are studied. A mathematical model is derived to simulate the magnetic wakes in a finite depth sea. Estimation of vessel traveling direction using single airborne sensors is reviewed and some problems in this method are remarked. A multi-sensor arrangement of magnetic transducers is proposed to remove these limitations. Estimation of vessel traveling direction with the proposed sensor configuration is performed. Robustness of the proposed method in dealing with Gaussian white noise and various target cutting angles is shown.