Little is known about the role of different water supplies in the diversity and publichealth significance of pathogenic protozoan parasites. Most of these organisms have beenubiquitous in waters worldwide. The numbers of waterborne infections indicate a significantrisk for their transmission even by drinking water. Hence, a total of 336 water sampleswere collected during 2009-2013 from different water sources from different areasof northern part of El-Minia Governorate, Egypt and were investigated for pathogenicprotozoa. 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). Thecommonest 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 histolytica/ dispar (8.73%) Giardia lamblia (6.35%) andNaegleria sp., (3.97%). Moreover, there were 14 samples with mixed parsitic infection:they were Cryptosporidium sp. and B. hominis in six samples, Cryptosporidium sp. andC. caytenensisin five samples and Cryptosporidium sp. and E. histolytica/dispar in threesamples. The most common contaminated 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.