Abstract The expansion of salmonid aquaculture has resulted in environmental challenges, including salmon lice that may infest both farmed and wild fish. For wild Atlantic salmon post-smolts that migrate from their rivers to the ocean, the first phase of their journey in the coastal zone, where aquaculture occurs, is critical when considering lice exposure. To evaluate the lice influence during the post-smot migration we have developed a migration model. An archive with spatiotemporal concentrations of lice larvae in Norwegian coastal waters has been established using a combination of state-of-the-art hydrodynamic and lice biology models. To estimate lice-induced mortality of wild salmon from Norwegian rivers, the infestation level on the virtual post-smolts was calibrated to match that observed on wild post-smolts genetically assigned their rivers of origin. The lice infestation pressure was modelled on post-smolts from 401 rivers covering all of Norway. Based on this, aquaculture-produced salmon lice-induced mortality of wild salmon post-smolts was estimated as <10% for 179 rivers, 10–30% for 140 rivers, and >30% for 82 rivers in 2019. Estimated mortalities were used together with other data sets to evaluate aquaculture sustainability in Norway. The aquaculture regulatory system represents a globally leading example of science-based management that considers the environmental impact.