A Hydrodynamic Vortex Separator (HDVS) has been modelled using Computational Fluid Dynamics (CFD) in order to predict the residence time of the fluid at the overflow and underflow outlets. A technique which was developed for use in Heating, Ventilation and Air Conditioning (HVAC) was used to determine the residence time and the results have been compared with those determined experimentally. It is shown that in using CFD, it is possible to predict the mean residence time of the fluid and to study the response to a pulse injection of tracer. It is also shown that it is possible to apply these techniques to predict the mean survival rate of bacteria in a combined separation and disinfection process.