We investigate the mechanisms by which microorganism that grow in the form of aggregates impact the permeability and the transport properties of porous media modeled as two-dimensional networks. In a companion paper <Dupin et al., this issue> we present a model of processes in a single channel. In this paper, we describe how to assemble channels into networks. Simple networks are investigated to identify phenomena of interest: four channels of different width operating in parallel to study the effect of local heterogeneity; a periodic network to quantify the effects of distance from the injection point on clogging and substrate utilization; and square lattice 5¿5 random width networks. Although square lattice random width networks are deemed better approximations of porous media, the simpler networks exhibit all the phenomena of interest, with the added advantage of these phenomena being decoupled. Results of numerical simulations for different network types under various boundary conditions show that aggregates have a far greater potential than biofilms to clog a porous medium. ¿ 2001 American Geophysical Union