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In order to understand and address the environmental impact of sonar and acoustic systems testing, the Naval Undersea Warfare Center (NUWC) and its partners are developing new techniques and applications for the passive classification and tracking of marine mammals in designated Navy acoustic sensor testing areas. The combined transient and broadband nature of the whale clicks contains a richly unique structure that can be exploited for completely non-evasive tracking and localization. NUWC has developed unique harmonic classification tools and other advanced visual tactical decision aids for the US Navy's latest sonar systems, designed to maximize operator performance and awareness of the undersea environment. In this paper, we explore the use of harmonic frequency and temporal-patterned structures in the detection and tracking of whales on the Atlantic Undersea Test and Evaluation Center (AUTEC) acoustic range. We demonstrate and report the results of the analysis of actual at-sea recorded blue whale vocalizations utilizing advanced sonar visualization and classification tools, and new tracking applications being developed.