Autonomous underwater vehicles (AUVs) used to locate multiple acoustic-tagged fish have previously been unable to alter their pre-programmed search paths to obtain precise position estimates. This problem is solved by the development of payload control software (Synthetic Aperture Override, SAOVR) that initiates maneuvers with trajectories favorable for estimating the tag's location from a synthetic aperture. Upon detecting a tag, SAOVR (running on an embedded guest computer) takes over navigation from the vehicle's native system after checking on constraints associated with the surrounding geography, timing, tag identification, signal strength, and current navigation state. Permitted maneuvers are then chosen from a template library and executed before returning the AUV to the initial deviation point to continue searching for other tags. This logic system is highly beneficial to AUV use for fish telemetry in challenging environments such as remote, narrow fjords. Any mission programmed with the AUV's native software can be run with SAOVR to allow scientists to easily implement and manipulate synthetic aperture geometries without altering any of the software.