© 2019, The Oceanographic Society of Japan and Springer Nature Singapore Pte Ltd. We found a good linear relation between the mean volume backscattering strength measured using a scientific echo sounder and the distribution density of moon jellyfish recorded simultaneously by an underwater video camera in small bays (Hokezu Bay and Mikame Bay) in Japan. This relation held in all of the surveys carried out in recent years (2013–2016), although the regression coefficient varied slightly from year to year due to the existence of ambient organisms. Using this relation and high-resolution echo sounder scan surveys across the bay, we obtained the spatial structures of moon jellyfish aggregations and categorized them into either patchy, layered, or wavy aggregations. We also examined possible physical mechanisms responsible for the moon jellyfish aggregations. In particular, passive particle tracking simulations of several idealized internal wave fields suggest that the formation of wavy aggregations is closely related to the presence of internal waves. However, internal waves alone cannot induce patchy and layered aggregations, indicating that particular biological processes (e.g., swimming behavior) are also necessary for such aggregations to form.