The inactivation of drinking water contaminated with bacteria requires a robust and effective technique. This can be achieved by using an appropriate inactivating material. Hence, the inactivation of Enterococcus faecalis bacteria using chitosan-based composites of bentonite clay was studied in a fixed bed column. The performance of the composite was evaluated as a function of initial bacterial concentration, bed mass and flow rate. The growth curves of E. faecalis were expressed as breakthrough curves (BTC), which were simulated using the logistic and Boltzmann models. The processed volume at breakthrough was used as performance indicator where it was revealed that the composite performed best at low bacterial concentration, low flow rate and large amount of bed mass. The sigmoidal patterns of both kinetic models were found to reproduce the experimental data adequately in various bacterial concentrations. It should also be pointed out that no leaching of the nanoparticles was found in the treated water, which makes the composite safe for treating drinking water.