Biofilm growth occurs in a variety of random porous media in a range of industrial processes; prediction of its growth and subsequent influence on hydrodynamics is hence desirable. In this study, we present the first numerical 3D pore-scale model of biofilm growth in porous media, based on a lattice Boltzmann simulation platform complemented with an individual-based biofilm model (IbM). We use it to explore the coupled interaction between nutrient mass transport, biofilm growth, and hydrodynamics. Biofilm is shown to be very effective at reducing the permeability of porous media, particularly under nutrient limited conditions. We conclude with a direct comparison of 3D and 2D biofilm growth simulations in porous media and show the necessity, of performing the simulations in 3D. (c) 2008 American Institute of Chemical Engineers AIChE J, 55: 494-504, 2009