This paper presents the design and development of a funnel-shaped Sparus Docking Station (SDS) intended for the non-holonomic torpedo-shaped Sparus II Autonomous Underwater Vehicles (AUV). The SDS is equipped with sensors and batteries, allowing for a stand-alone long-term deployment of the AUV. An inverted Ultra Short BaseLine (USBL) system is used to locate the Docking Station (DS) as well as to provide long-term drift-less AUV navigation. The SDS is able to observe the ocean currents using a Doppler Velocity Log (DVL), being motorized to allow its self-alignment with the current. Moreover, a docking algorithm accounting for the current is used to guide the robot during the docking maneuver. The paper reports experimental results of the docking maneuver in sea trials.