The rapid development of intensive fish farming has been associated with the spreading of infectious diseases, pathogens and parasites. One such parasite isSparicotyle chrysophrii(Platyhelminthes: Monogenea), which commonly infects cultured gilthead seabream (Sparus aurata)—a vital species in Mediterranean aquaculture. The parasite attaches to fish gills and can cause epizootics in sea cages with relevant consequences for fish health and associated economic losses for fish farmers. In this study, a novel stratified compartmental epidemiological model ofS. chrysophriitransmission was developed and analysed. The model accounts for the temporal progression of the number of juvenile and adult parasites attached to each fish, as well as the abundance of eggs and oncomiracidia. We applied the model to data collected in a seabream farm, where the fish population and the number of adult parasites attached to fish gills were closely monitored in six different cages for 10 months. The model successfully replicated the temporal dynamics of the distribution of the parasite abundance within fish hosts and simulated the effects of environmental factors, such as water temperature, on the transmission dynamics. The findings highlight the potential of modelling tools for farming management, aiding in the prevention and control ofS. chrysophriiinfections in Mediterranean aquaculture.