Biofilms are complex biologic structures formed by coordinated, functional microbial communities and capable of adhering and growing on virtually any surface. Thorough understanding of material properties and hydrodynamic interactions of biofilms can account for critical advances in the development of systems capable of full functioning in biochemically active mediums resulting in minimum environmental issues and optimization of existing materials and technologies.The classical modelling of biofilm proposed by Picioreanu et al. (1998a, b) combined conventional cellular automaton and mathematical population models aiming to describe both colony growth and qualitative pattern formation associated with different environmental settings. It does not, however, account for microorganism diversity and intra/extra cellular exchanges which influence directly on biofilm structure. Current approaches to biofilm simulation include an extension of the Individual based Modelling (IbM) method which was originally designed for planar microbial communities. This method, tough, is highly computationally demanding and lacks integration between macro and micro bio-fluidic processes being not feasible for large scale simulation.