Maintaining the dispersal and connectivity of marine plants, such as seagrasses, supports the replenishment and recovery of populations and the recolonization of unoccupied habitat patches. We simulated dispersal and connectivity of seagrasses in the Torres Strait by using a biophysical modelling approach to combine a hydrodynamic model of water circulation with biological parameters that defined the attributes of multiple species. The simulations released millions of passive ‘virtual’ propagules at known sites of seagrass presence and were timed to capture variability in winds, currents and tides over three reproductive periods. Simulation outputs were used in a network analysis to identify the location and intensity of connections between seagrass habitat patches. Network analysis was also used to explore changes to the structure and functioning of the seagrass network when patches were removed due to cumulative disturbance events. The outputs of our analysis can inform the development of quantitative objectives and conservation strategies to protect seagrass connectivity in the Torres Strait by identifying critical stepping stones and source meadows. In addition, model outputs enabled an improved understanding of the impact of cumulative disturbance events on the functioning and health of seagrass in the Torres Strait.