Pathogen control during poultry processing critically depends on more enhanced insight into contamination dynamics. In this study we build an individual based model (IBM) of the chilling process. Quantifying the relationships between typical Canadian processing specifications, water chemistry dynamics and pathogen levels both in the chiller water and on individual carcasses, the IBM is shown to provide a useful tool for risk management as it can inform risk assessment models. We apply the IBM to Campylobacter spp. contamination on broiler carcasses, illustrating how free chlorine (FC) sanitization, organic load in the water, and pre-chill carcass pathogen levels affect pathogen levels of post-chill broilers. In particular, given a uniform distribution of Campylobacter levels on incoming poultry we quantify the efficacy of FC control in not only reducing pathogen levels on average, but also the variation of pathogen levels on poultry exiting the chill tank. Furthermore, we demonstrate that the absence/presence of FC input dramatically influences when, during a continuous chilling operation, cross-contamination will be more likely.