The North Sea faces intense ship traffic owing to increasing human activities at sea. As harbour seals (Phoca vitulina) are abundant top predators in the North Sea, it is hypothesised that they experience repeated, high-amplitude vessel exposures. Here, we test this hypothesis by quantifying vessel noise exposures from deployments of long-term sound and movement tags (DTAGs) on nine harbour seals from the Wadden Sea. An automated tool was developed to detect intervals of elevated noise in the sound recordings. An assessment by multiple raters was performed to classify the source as either vessels or other sounds. A total of 133 vessel passes were identified with received levels >97 dB re 1µPa RMS in the 2 kHz decidecade band and with ambient noise >6 dB below this detection threshold. Tagged seals spent most of their time within Marine Protected Areas (89 ± 13%, mean ± SD) and were exposed to high-amplitude vessel passes 4.3 ± 1.6 times per day. Only 32% of vessel passes were plausibly associated with an AIS-registered vessel. We conclude that seals in industrialized waters are exposed repeatedly to vessel noise, even in areas designated as protected, and that exposures are poorly predicted by AIS data.