Outbreaks of disease caused by the infectious salmon anemia virus (ISAV) are an important threat to Atlantic salmon aquaculture production. Pathogen dispersal from an infected farm into the surrounding ocean poses further risks of infection to wild fish and other farms but is difficult to predict. This study aimed to build a framework using ocean circulation and particle tracking models in conjunction with a dynamic infection model and virus inactivation model to simulate the waterborne dispersal of ISAV from Atlantic salmon farms in the Quoddy Region (QR, New Brunswick, Canada and Maine, USA). Using a particle tracking method , simulated particles were released from hypothetically infected farms at rates estimated by a dynamic infection model, and were then advected by modelled currents. Inactivation of viral cohorts by ambient ultraviolet (UV) radiation and natural microbial communities was simulated during advection. Simulations were conducted on thirteen farms in the QR area to demonstrate this modelling system. Maps showing hypothetical spatiotemporal changes of viral concentrations in ambient water were produced for farms under simulated worst-case scenario outbreaks. The advection distances of infectious particles were calculated. A farm connectivity matrix in terms of viral infection was produced, with mutual and asymmetrical connectivity patterns identified between farms. Factors that impact the simulation of viral shedding and inactivation, hydrodynamic effects on dispersal, model application to aquaculture management, and future development were discussed. This framework provides an approach and opportunities to simulate waterborne viral transmission by considering the biology and epidemic features of significance for pathogens and dynamic ocean conditions.