Underwater acoustic (UWA) multi-user network algorithms can only be fully tested through experimental studies where communication signals are transmitted through a real underwater channel. Reconfigurable UWA modem provides a flexible environment for the testing of different communication algorithms including networking protocols. In this paper we present design, implementation, and testing of a physical layer algorithm on reconfigurable acoustic modem. This physical layer is very flexible; therefore it can easily be modified in order to be employed for the testing of different UWA networking algorithms.