ABSTRACT: Global aquaculture production continues to increase across a variety of sectors, including Atlantic salmon production in Scotland. One limitation to the expansion of open-cage aquaculture is disease-induced stock losses as well as the potential for disease agents from farms interacting with other farms and possibly with wild salmonids. Epidemiological studies of disease-agent transmission often omit environmental transmission of organisms, although this process is an integral part of parasite spread and incidence. Within the aquatic environment, water movements enable pathogens and parasites to potentially be transmitted over long distances. As pathogens and parasites are transported, their status can change; they can degrade or, in the case of sea lice, develop into an infectious stage. A combination of biological and physical models is required to understand the transmission of disease-causing organisms. Here we propose a set of components that have been implemented in a range of modelling studies of sea lice dispersal, and describe how such attributes have been used in developing a study in one of Scotland’s largest fjordic systems. By developing descriptive simulation model frameworks, which are validated using physical and biological observations, alternative methods of integrated pest management can be investigated and developed. The identification of dispersal routes of sea lice and establishment of potential farm-farm connections can inform sea lice management.