Contributions and effects of anthropogenic activities on the underwater soundscape of the sub-Antarctic regions remain poorly studied. Over a 21-month period (April 2021 to December 2022), we recorded underwater noise levels amid two sub-Antarctic Prince Edward Islands (PEIs) within an offshore marine protected area with the aim to quantitatively investigate the sources of underwater noise and the impact of such noise on the detectability of marine mammal vocalizations. We measured underwater noise levels within the low (20–120 and 121–800 Hz), medium (801–25 000 Hz) and high (25 001–48 000 Hz) frequency bands. Wind speed was the primary predictor of low and medium frequency underwater noise levels, whereas iceberg volume was the primary predictor at the high frequency band. Probabilities of detecting vocalizations of Antarctic blue, fin, humpback, Antarctic minke and killer whales decreased with increasing noise levels. On the contrary, probabilities of detecting sei and Madagascan pygmy blue whale vocalizations increased with noise levels. Overall, these novel results indicate that geophonic noise dominates the underwater soundscape of the PEIs in the absence of intense anthropogenic activities such as marine traffic, and that the detectability of marine mammal underwater vocalizations is species-specific.