The impact of the noise radiated from merchant ships on marine life has become an active area of research. In this paper, a methodology integrating observation at a single location and modelling the whole noise field in shallow waters is presented. Specifically, underwater radiated noise data of opportunistic merchant ships in the waters of Zhoushan Archipelago were collected at least one day in each month from January 2015 to November 2016. The noise data were analyzed and a modified empirical spectral source level (SSL) model of merchant ships was proposed inspired by the RANDI-3 model (Research Ambient Noise Directionality) methodology. Then combining the modified model with the realistic geoacoustic parameters and AIS data of observed merchant ships, the noise mappings in this area were performed with N×2D of Normal Mode calculations, in which the SSL of each ship was estimated using the modified model. The sound propagation at different receiving positions is different due to the shielding effect of islands and bottom topography. The methodology proposed in this paper may provide a reference for modelling shipping noise in shallow waters with islands and reefs.