Rotavirus group A (RV-A) and Cryptosporidium spp. are recognized as important pathogens causing gastroenteritis, even with very low doses in all age groups and representing a public health risk. Seventy-two wastewater samples were collected and concentrated for detecting Cryptosporidium spp. and RV-A. PCR was performed for identification of genus Cryptosporidium using generic primers and species specific primers for Cryptosporidium parvum / Cryptosporidium hominis. Multiplex seminested RT-PCR was performed to identify the genotypes P and G of RV-A. Our findings showed that the rotavirus genome was detected in 29 (40.3%) out of 72 analyzed wastewater samples. Rotavirus rates in raw wastewater samples were higher (47.2%) than those detected in treated wastewater (33.3%). Cryptosporidium was found in 33.3% of 72 tested wastewater samples. All Cryptosporidium-positivesamples were related to Cryptosporidium parvum. The prevalence of Cryptosporidium parvum in influents and effluents reached 41.7% and 25%, respectively. The removal rates of rotavirus and Cryptosporidium parvum in the examined WWTP were 29.4% and 40%, respectively. The largest percentage of positive rotavirus in raw wastewater samples was detected in winter (77.8%), followed by 66.7% in autumn. Three P types and two G types of RV-A strains were identified in wastewater samples. The most prevalent types of RV-A strains in raw and treated sewage samples were G1 and P[8] genotypes. In conclusion, wastewater treatment processes, including a trickling filter, were not sufficient to eliminate several RV-A strains and Cryptosporidium parvum, leading to the potential release of these pathogens from domestic sewage into water sources.