This paper describes a communication and localization system for micro-autonomous underwater vehicles (µAUVs) undertaking monitoring and mapping tasks in nuclear storage ponds. A distinctive feature of this underwater environment is the severe multipath propagation and long reverberation times. The paper describes how a common code division multiplexed signal format is used to mitigate the acoustic channel impairments to achieve both communication and localization. The system consists of an onshore base-station, equipped with a four-element distributed transceiver antenna, and underwater acoustic modems installed in the µAUVs. The system simultaneously provides positioning of a swarm of µAUVs, with addressed transmission of navigation commands from the base-station to µAUVs, and telemetry data transmission to the base-station from the µAUV.