The subsurface leaching of soluble chemicals in a fractured porous medium poses long-term risk of groundwater contamination. Tracing the occurrence, movement and consequences of such hydro-geo-chemical interactions is the fundamental process for an effective remediation plan. However, the complexity of geomorphology and mass transfer mechanisms makes it challenging while addressing these issues in a real field scale. The present study focuses on simulating the concentration profile of nitrate elution in a pseudo two-dimensional coupled fracture-skin-matrix system under active biodegradation using an implicit finite difference numerical technique. The interface between the fracture and rock matrix is assumed to possess a skin with time-varying porosity imitating the effect of bio-clogging. The results indicate that denitrification is significant in reducing the dissolved nitrate concentration for initial skin porosity of 10% in the presence of an unlimited oxygen and primary substrate. When the rate of change of skin porosity remains lower with a minimal variation, the nitrate concentration provided a considerable reduction in the vicinity of the fracture inlet. A similar trend is observed for dissolved oxygen concentration as well. The concentration profile of nitrate showed a higher rate of reduction with an increase in initial skin porosity value from smaller to significantly larger values. The present study clearly indicates the role of skin interface in depicting the solute concentration profile in fracture, especially during the washout of bio-clogged membrane (biofilm) attached to the rock matrix. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.