Monitoring of BTX natural attenuation in a fractured rock aquifer is highly challenging due to lack of knowledge about the influence of interaction of heterogeneous domains on transport processes. Contaminant transport in a fractured rock is commonly investigated using dual continuum models by considering fracture and its surrounding rock–matrix as two different continuums. In this study, a numerical multi-component transport model based on a triple continuum modeling approach is developed to investigate the transport of dissolved BTX in a discretely fractured aquifer with fracture–skin. A residual BTX source zone is considered to be present at the fracture inlet. A multi-component dissolution model is coupled with the present numerical model to simulate the dissolution of benzene, toluene and xylene at the residual BTX source. Dissolved BTX components are considered to undergo sorption and biodegradation in addition to advection and dispersion within the fracture. Dissolved BTX components diffusing to fracture–skin and rock–matrix are considered to undergo sorption and biodegradation in fracture–skin and rock–matrix. A novel sensitivity analysis approach based on spatial moments is introduced in the manuscript to investigate the sensitivity of various flow and transport parameters of fracture–skin and rock–matrix on dissolved BTX mass retained in fracture and matrix. The presence of fracture–skin is found to significantly affect the concentration distribution and mass retention of dissolved BTX components in a fractured aquifer. © 2017, Springer-Verlag GmbH Germany.