In this paper, a novel approach to provide full autonomy in the control and synchronization of multiple payload sonar systems is described, facilitating the close-proximity integration and concurrent operation of multiple high-frequency acoustic sensors on an unmanned underwater vehicle. Recent advances in computational technology and real-time programming techniques afford the ability to process bathymetric data in situ to react to real-time environment data. The novel approach presented interrogates real-time bathymetric data to predict the transmission-reception timing of payload sensor acoustic pulses, thus permitting the ability to synchronize the trigger of the instruments such that neighboring return signals of other sonar are not saturated by sensor crosstalk.