While biological clogging of porous systems can be problematic in numerous processes (e.g., microbial enhanced oil recovery-MEOR), it is targeted during bio-barrier formation to control sub-surface pollution plumes in ground water. In this simulation study, constant pressure drop (CPD) and constant Volumetric flow rate (CVF) operational modes for nutrient provision for biofilm growth ill a Porous system are considered with respect to optimum (minimum energy requirement for nutrient provision) permeability reduction for bio-barrier applications. Biofilm growth is Simulated using a Lattice-Boltzmann (LB) simulation platform complemented with an individual-based biofilm model (IbM). A biomass detachment technique has been included using a fast marching level set (FMLS) method that models the propagation of the biofilm-liquid interface with a speed proportional to the adjacent velocity shear field. The porous medium permeability reduction is simulated for both operational modes using a range of biofilm strengths. For stronger biofilms, less biomass deposition and energy input are required to reduce the system permeability during CPD operation, whereas CVF is more efficient at reducing the permeability of systems containing weaker biofilms. Biotechnol. Bioeng. 2009;103: 767-779. (c) 2009 Wiley Periodicals, Inc.