A finite-element reactive transport model is developed and applied to study the transport behaviour of nitrate under the effect of denitrification in saturated fractured media. The reduction of nitrate is considered to be undertaken by a heterotrophic population of bacteria present on the fracture walls and in the pore space of the porous matrix. The bacterial metabolic activity is controlled by the availability of an electron donor (organic matter) and electron acceptors (nitrate and oxygen). Model equations are developed assuming 1D advective–dispersive transport in a set of parallel fractures with 2D diffusive transport in the adjacent porous matrix. The bacterial reaction in these equations is represented by dual Monod kinetic terms and the bacterial growth is represented by a single linear kinetic equation. The equations are discretized by the finite-element Galerkin method and the resultant set of non-linear algebraic equations is solved by an iterative scheme. The model is used to explore the effect of denitrification on fracture and porous matrix nitrate concentration profiles for different values of fracture aperture size, advective velocity, porous matrix width, porosity, and dispersion and diffusion coefficients. The effect of the presence of oxygen in limiting rates of bacterial nitrate reduction is also assessed. Overall, it is concluded that in fractured media with good porous matrix diffusion properties and favourable properties for bacterial growth, denitrification in the porous matrix can be more significant than in the fracture set in the reduction of nitrate mass.