Underwater control applications, such as control of Autonomous Underwater Vehicles (AUV)s, have recently gained significant interest, and there is a growing demand for high-speed wireless communication between AUVs and base station. Acoustic communication provides low data rates and high propagation delays, both of which are not suitable for employing high control gains for the navigation of AUVs. On the other hand, Radio Frequency (RF) communication provides high data rate, but it is constrained by high attenuation due to high conductivity and permittivity of water resulting in a short working range. In this work, we propose an underwater networked control system with acoustic and RF hybrid communication, where an acoustic link is employed for long range communication and RF link is applied in close range. Our performance results indicate that the acoustic and RF hybrid communication system takes up to 38.5% less time to dock, up to 91% smaller steady state error and spends up to 39% lower communication energy as compared to the acoustic only system at the expense of up to 22.35% higher motive energy.