Little is known about the role of different water supplies in the diversity and public health significance of pathogenic protozoan parasites. Most of these organisms have been ubiquitous in waters worldwide. The numbers of waterborne infections indicate a significant risk for their transmission even by drinking water. Hence, a total of 336 water samples were collected during 2009-2013 from different water sources from different areas of northern part of El-Minia Govemnorate, Egypt and were investigated for pathogenic protozoa. They were examined by direct microscopy followed by Modified Ziehl- Neelsen and Giemsa stains. 140 samples (41.7 %) were positive (statistically significant; P value P<0.0003). Prevalence rates were in Summer (66.7%/), Spring (51.1%), Fall (26.2 %) and Winter (22.6%). These data were statistically significant (P<0.0001). The commonest protozoa detected as a single infection was Cryptosporidium sp. (53.17%) found in all water supplies, followed by Blastocystis hominis (15.87%), Cyclospora caytenensis (11.9%), Entamoeba hiseolytica/dispar (8.73%) Giardia lamblia (6.35%() and Naegleria sp., (3.97%). Moreover, there were 14 samples with mixed parsitic infection: they were Cryptosporidium sp. and B. hominis in six samples, Cryptosporidum sp. and C. caytenenisin five samples and Cryptosporidium sp. and E histolytica/dispar in three samples. The most common contamninated water source was ponds where 32 samples (66.7%) were-positive followed by canal water 30 samples (62.5%). The results were discussed and the recommendations were offered.