In this study, underwater noise from a full-scale wave energy converter system (ISWEC), installed on the coast of Pantelleria Island (central Mediterranean Sea), was characterized. The noise was measured using an autonomous acoustic recorder anchored to the sea bottom 40 m from the ISWEC hull. Acoustic monitoring continued for 15 months, starting 7 months before (PRE), 2 months during (INST) and 6 months after the ISWEC installation (POST). The levels of noise, assessed with power spectrum density and octave and third-octave band sound pressure levels (BSPLs), were higher during the POST period than during the PRE period at lower frequencies up to 4 kHz and increased with wave height. During the ISWEC activation for energy production (POST_ON) in the wave height range 1–2.9 m, the BSPLs increased much more at lower frequencies up to 4 kHz (the median BSPLs at 63 Hz for the PRE, POST, and POST_ON conditions were 73, 106, and 126 dB re 1μPa, respectively). Considering the biophonies that make up the soundscape of the area, we examined the possible masking of fish choruses due to ISWEC noise and highlighted that at a distance of 1000 m, the 800 Hz peak frequency was 10 dB above the ISWEC signal. Within this distance from ISWEC, a possible masking effect is supposed.