Underwater acoustic sensor networks face unique challenges in the design and development of communication and network protocols, because of the inherently different characteristics of water as a medium for signal propagation. In the mobile sink architecture, a mobile sink that traverses the network to transfer non delay-sensitive data from the sensors directly and avoid multi-hop transmissions. An area partitioning algorithm is proposed in this paper to divide the network in regions to minimize the traveling distance of the sink and the formation of clusters that maximize the throughput. A transmission mechanism based on superposition coding is developed to increase the throughput of downlink control messages to the sensors. Finally, a MAC protocol is developed to facilitate the transmissions.