One of the United Nations Sustainable Development Goals regarding “conservation and sustainable use of the oceans, seas, and marine resources” emphasizes the urgency of eliminating harmful effects on the sea and its biota, where the role of anthropogenic activities is crucial. The global trend of merchant shipping is increasing, thus enlarging underwater noise levels. As a result, greater noise can harm aquatic animals in their habitats. In the Baltic Sea, the underwater sound pressure levels are now being evaluated utilizing noise measurement, modelling, and mapping. In areas such as narrow ship passages, namely lagoons, channels, or straits, the ambient underwater noise modelling becomes very complex, even though these EU inland waters are regarded by legislation as part of the marine basin. For instance, the Klaipėda Channel (Klaipėda Strait), connecting the Baltic Sea and the Curonian Lagoon, is regarded by the national Lithuanian legislation as part of marine waters, where the environmental status should be evaluated according to the EU Maritime Strategy Framework Directive. In this narrow channel, an alternative to the modelling of ambient sound pressure levels can be applied to understand the long-term trends of vessel-sourced noise emissions. In this paper, an example of application of ship noise emission modelling for a narrow Klaipėda Harbour area is presented, along with the results obtained throughout 2015–2017. The modelled noise levels in the harbour area reached the median levels of 112.5 dB in 2015 and 102.6 dB re 1 µPa2 in 2017. The maximum emitted instantaneous sound pressure levels by ships reached 173.7 dB in 2015 and 179.4 dB re 1 µPa2 in 2017 in the area of interest.