Underwater sensor networks consist of sensors and vehicles deployed to perform collaborative monitoring tasks over a given region. Underwater sensor networks will find applications in oceanographic data collection, pollution monitoring, offshore exploration, disaster prevention, assisted navigation, tactical surveillance, and mine reconnaissance. Underwater acoustic networking is the enabling technology for these applications. In this paper, an architecture for three-dimensional underwater sensor networks is considered, and a model characterizing the acoustic channel utilization efficiency is introduced, which allows investigating some fundamental characteristics of the underwater environment. In particular, the model allows setting the optimal packet size for underwater communications given monitored volume, density of the sensor network, and application requirements. Moreover, the problem of data gathering is investigated at the network layer by considering the cross-layer interactions between the routing functions and the characteristics of the underwater acoustic channel. Two distributed routing algorithms are introduced for delay-insensitive and delaysensitive applications. The proposed solutions allow each node to select its next hop, with the objective of minimizing the energy consumption taking the varying condition of the underwater channel and the different application requirements into account. The proposed routing solutions are shown to achieve the performance targets by means of simulation.