Cryptosporidium parvum and Giardia lamblia are two of the most chlorine resistant microorganisms with notable adverse effects on humans. Our study shows that waters containing these two protozoa at low concentrations can be efficiently disinfected in continuous flow by using a commercial fibrous ceramic TiO2 photocatalyst. The efficiency of the photocatalytic disinfection is largely enhanced by adding a small concentration of chlorine. In this way, the residence time on the photoreactor can be considerably shortened. In contrast, under the same conditions and radiance power, UV light without any photocatalyst is significantly less efficient, particularly for G. lamblia. These results exemplify the advantages of the photocatalytic process for safe and complete water disinfection.