A numerical model is developed for describing the transport of virus in a fracture-matrix coupled system with fracture-skin. An advective dispersive virus transport equation, including first-order sorption and inactivation constant is used for simulating the movement of viruses. Implicit finite-difference numerical technique is used to solve the coupled non-linear governing equations for the triple continuum model consisting of fracture, fracture-skin and the rock-matrix. A varying grid is adopted at the fracture and fracture-skin interface to capture the mass transfer. Sensitivity analysis was performed to investigate the effect of various properties of the fracture-skin as well as viruses on the virus concentration in the fractured formation with fracture-skin. Simulation results suggest that the virus concentration in the fracture decreases with increment in the fracture-skin porosity, fracture-skin diffusion coefficient, mass transfer coefficient, inactivation constant and sorption distribution coefficient, and with reduction in the fracture aperture. © 2012, China University of Geosciences (Beijing) and Peking University. Production and hosting by Elsevier B.V. All rights reserved.