Information on biodiversity is essential to evaluate the ecological status of coral reefs. Sounds produced by reef-associated organisms have been used as a biodiversity indicator. However, the interference from abiotic sounds and the lack of a comprehensive audio library have impeded effective evaluation. This study investigated the application of underwater soundscapes as a remote-sensing method to detect biological and anthropogenic activities. Using techniques including the visualization of long-duration recordings, source separation, and clustering, soundscapes were separated into sounds of anthropogenic and biological sources. Our results revealed the dynamics of biological sounds among coral reefs off Sesoko Island, Okinawa, Japan. Biological sounds were much more prominent in shallow-water reefs than in upper-mesophotic reefs, but their spectral features and compositions differed. The shallow-water reefs were dominated by broadband sounds of crustaceans and low-frequency transient fish calls, whereas the upper-mesophotic reefs were characterized by a diverse array of fish choruses and transient sounds. We also discovered that shipping noise heavily interfered with the soundscapes from the upper-mesophotic reefs and represented an invisible threat to life in the low-light habitat. The applied techniques of soundscape information retrieval revealed the distinct ecological status of coral reefs and the behavior change of sound-producing organisms in high temporal resolution. Implementation of soundscape monitoring can generate ecological information on habitat quality, reef biodiversity, human activities, and their interactions. Global collaboration on underwater soundscapes will establish a data-informed platform and help stakeholders assess the resilience of coral reefs to environmental and anthropogenic stressors.