Recreational boating is an increasing activity in coastal areas and its spatiotemporal overlap with key habitats of marine species pose a risk for negative noise impacts. Yet, recreational vessels are currently unaccounted for in vessel noise models using Automatic Identification System (AIS) data. Here we conduct a case study investigating noise contributions from vessels with and without AIS (non-AIS) in a shallow coastal area within the Inner Danish waters. By tracking vessels with theodolite and AIS, while recording ambient noise levels, we find that non-AIS vessels have a higher occurrence (83%) than AIS vessels, and that motorised recreational vessels can elevate third-octave band noise centred at 0.125, 2 and 16 kHz by 47–51 dB. Accordingly, these vessels dominated the soundscape in the study site due to their high numbers, high speeds and proximity to the coast. Furthermore, recreational vessels caused 49–85% of noise events potentially eliciting behavioural responses in harbour porpoises (AIS vessels caused 5–24%). We therefore conclude that AIS data would poorly predict vessel noise pollution and its impacts in this and other similar marine environments. We suggest to improve vessel noise models and impact assessments by requiring that faster and more powerful recreational vessels carry AIS-transmitters.