Experimental results indicate that EPS on bacterial surfaces or substratum surfaces are involved in different stages of bacterial colonization. Without biofilm coating, distribution of attached bacteria on the column media as a function of transport distance exhibited non-monotonic deviation from classic colloid filtration theory (CFT), which can be attributed to bacterial re-entrainment and the steric interactions between bacterial surface extracellular polymers and glass beads. Bacterial deposition behavior in the biofilm mediated columns differed significantly from that observed in the clean column media. With thin biofilm accumulation, biofilm surface hydrophobicity and polymer interactions between biofilm surface EPS and bacteria play important roles in controlling bacterial adhesion; while porous media physical and hydrodynamic changes as a result of biofilm growth become significant when biofilm accumulates to a certain thickness. Prolonged persistence of newly introduced bacteria within the biofilm matrix was observed using both culture methods and molecular techniques. Newcomer bacteria could become an integral part of indigenous biofilm after initial colonization, and biofilm detachment was the phenomenon most likely influencing the fate of newcomer bacteria and the down stream water qualities. Findings of this study suggest that biofilm plays a significant role in controlling the fate of bacteria in porous media, and that the interaction between bacteria and biofilm surfaces should be considered when predicting bacterial and pathogen migration in the environment.