Salmon aquaculture in Scotland continues to increase; however, one of the potential limitations to its further sustainable growth is the ectoparasitic sea louse Lepeophtheirus salmonis. The industry in Scotland undertakes coordinated management procedures to control the levels of sea lice on farms in designated production areas. We developed a biophysical sea lice dispersal model for Loch Linnhe, one of the largest fjords on the west coast of Scotland, to provide further information to help establish more effective farm management areas. We successfully extend modelling principles previously applied to a small Scottish fjordic system. Modelling scenarios demonstrate heterogeneity in the distribution of sea lice within the system and simulations, suggesting that lice could be transmitted up to 30 km. The scenarios are assessed by comparing model predictions against lice sampled by both planktonic trawls and settlement on sentinel caged fish. The model predicts the ranked abundance of both planktonic and settled lice assuming that the lice input to the system is relative to host biomass. Data collection is ongoing for undertaking and assessing additional scenarios. © 2013 Crown copyright.