Underwater soundscapes, though invisible, are crucial in shaping the biodiversity of marine ecosystems by acting as habitat‐specific settlement cues for larvae. The deep sea has received little attention in soundscape research, but it is being targeted for mineral extraction to feed the ever‐growing needs of our society. Anthropogenic impacts on soundscapes influence the resilience of key shallow‐water habitats, and the same likely applies to the deep. Japan is a forerunner in deep‐sea mining, but virtually no deep soundscape baselines exist for Japanese waters. Here, we report baseline soundscapes from four deep‐sea locations in Japan, including the Suiyo Seamount hydrothermal vent, the abyssal plain around the Minamitorishima Island home to manganese nodule fields and muds rich in rare‐earth elements, twilight depths off Sanriku, as well as a typical bathyal system in Suruga Bay. Long‐duration audio recordings were visualized and factorized by an unsupervised machine learning model, revealing differing characteristics among the habitats. Two locations near the coast are highly influenced by shipping noise. The Suiyo vent is characterized by low‐frequency sounds from venting, and the abyssal Minamitorishima is quiet with a flat spectral shape. Noise from observation platforms is likely sufficient to alter soundscape characteristics, especially in offshore locations, suggesting offshore mining‐targeted areas are susceptible to impacts from anthropogenic noise. We argue that the monitoring of soundscapes is an indispensable component for assessing potential mining impacts on deep‐sea ecosystems. Our results establish reference points for future soundscape monitoring and assessment in Japanese waters as well as similar ecosystems globally.