The objective of this study is to analyse the movement of nitrates and dissolved oxygen under the effect of denitrification in a fracture–matrix (F–M) system with skin formation. An implicit finite difference scheme is developed to model the coupled nonlinear partial differential equations. A varying grid is considered at the fracture–skin interface to handle the mass transfer from the fracture to the skin. Bacterial growth is taken into account in the fracture. The growth is affected by the presence of electron donor and electron acceptor. Sensitivity analysis is performed for various fluid flow velocities, skin diffusion coefficients, facture dispersion coefficients, skin porosities (S-P), fracture apertures and rock–matrix (R–M) porosities. Outcomes of this study indicate that the occurrence of skin enriches the transport of nitrates as compared to the absence of skin when denitrification process exists in the system. The low fluid velocity (0.5 m/day) reduces the transport of nitrates to a distance of 5 m, whereas a high fluid velocity (5.0 m/day) triggers up to a distance of 30 m from the fracture inlet. The higher skin diffusion coefficient enhances the migration of nitrates and dissolved oxygen compared to the lower skin diffusion coefficients. The fracture aperture variation from 100 to 500 μm increases the movement of nitrates and dissolved oxygen in fracture from 4 to 10 m, respectively. The variation of S-P from 25 to 75% also follows the same trend. Variation in R–M porosity has an insignificant effect on the movement of nitrates and dissolved oxygen. © 2021, King Fahd University of Petroleum & Minerals.