A mechanistic mathematical model was developed that successfully traced the Cr(VI) concentration profiles inside porous aquifer media columns. The model was thereafter used to calculate Cr(VI) removal rate for a range of Cr(VI) loadings. Internal concentration profiles were modelled against data collected from intermediate sample ports along the length of the test columns. For the first time, the performance of a simulated barrier was evaluated internally in porous media using a finite difference approach. Parameters in the model were optimised at transient-state and under near steady-state conditions with respect to biomass and effluent Cr(VI) concentration respectively. The best fitting model from this study followed non-competitive inhibition kinetics for Cr(VI) removal with the best fitting steady-state parameters: Cr(VI) reduction rate coefficient, k = 5.2×10-8 ℓ∙mg−1∙h−1; Cr(VI) threshold inhibition concentration, C = 50 mg∙ℓ−1; and a semi-empirical reaction order, n = 2. The model results showed that post-barrier infusion of biomass into the clean aquifer downstream of the barrier could be limited by depletion of the substrates within the barrier. The model when fully developed will be used in desktop evaluation of proposed in situ biological barrier systems before implementation in actual aquifer systems.