Protozoal water contamination is an alarming cause of countless waterborne outbreaks. The most
eminent causal protozoa are Cryptosporidium and Giardia species (spp.) as they can endure aquatic
environment even with chlorine disinfectants. The currently used traditional techniques cannot permit
an easy detection of the waterborne protozoa concerning their count, viability, and pathogenicity. The
present work detected protozoal contamination of the drinking water in Egypt with the determination
of their load, viability and potential pathogenicity. Four techniques were compared including conventional
staining techniques, immunofluorescence (IF) staining, flow cytometry (FC) and molecular
study. Also, viability was assessed by conventional trypan blue stain and nucleic acid stain. Along a
year, 64 water samples were collected and concentrated from water tanks and tap water of different
districts, significant differences (P < 0.001) was between the different techniques in each season regarding
the detection of Giardia cysts and Cryptosporidium oocysts. Number of total positive samples
was significantly higher in tank water than tap water (P < 0.001) especially at summer. Flow cytometry
and nested polymerase chain reaction (nPCR) proved to be much more sensitive than IF assay, and
conventional staining techniques. Regarding viability, nucleic acid stain was more sensitive than trypan
blue stain (P < 0.001). Also, C. parvum predominate other Cryptosporidium genotypes.