Recent Cryptosporidium outbreaks have highlighted concerns about filter efficiency and in particular particle breakthrough. It is essential to ascertain the causes of Cryptosporidium sized particle breakthrough for Cryptosporidium cannot be destroyed by conventional chlorine disinfection. This research tried to investigate the influence of temperature, flow rate and chemical dosing on particle breakthrough during filtration. The results showed that higher temperatures and coagulant doses could reduce particle breakthrough. The increase of filtration rate made the residual particle counts become larger. There was an optimal dose in filtration and was well correlated to ζ potential.