Marine mammals are very seldom detected and tracked acoustically at different depths. The air contained in body cavities, such as lungs or swimbladders, has a significant effect on the acoustic energy backscattered from whale and fish species. Target strength data were obtained while a humpback whale (Megaptera novaeangliae) swam at the surface and dove underneath a research vessel, providing valuable multi-frequency echosounder recordings of its scattering characteristics from near surface to a depth of about 240 m. Increasing depth dramatically influenced the backscattered energy coming from the large cetacean. This study is tightly linked to the ultimate goal of developing an automated whale detection system for mitigation purposes.