Cryptosporidium and Giardia are one of the most prominent parasitic protozoans found in wastewater treated by wastewater treatment plants (WWTPs). They cause Cryptosporidiosis and Giardiasis respectively, which can be fatal in immuno-compromised individuals. Thus, their removal by WWTPs is essential. This study aimed at investigating the prevalence of Crytposporium and Giardia through treatment processes at two South African wastewater treatment plants and assessing the efficiency of the WWTPs in removing them. A total of 162 samples (54 raw influents, 36 primary treated effluents, 36 secondary treated effluents and 36 final treated effluents) were collected from two South African WWTPs over a period of one year. Results obtained from the study show that Cryptosporidium was detected in 98% (159/162) of the samples collected, whilst Giardia was detected in 99% (160/162) of the samples collected from both wastewater treatment plants. Both Crytposporium and Giardia were detected in 100% (n=54) of raw influent samples. The same result was obtained in primary treated effluent, where both Cryptosporidium and Giardia was detected in 100% (n=36) of the samples collected. In secondary treated effluent, 36 samples were collected and Cryptosporidium was detected in 94% of the samples, whereas Giardia was detected in 100% of the samples. In the final treated effluent samples, both Cryptosporidium and Giardia where detected 97% (n=36) of the samples collected. Detection of Cryptosporidium and Giardia in most of the wastewater treatment stages indicated these parasites are prevalent in the two WWTPs. Although the two WWTPs showed high removal of the two parasites in wastewater, their presence in the final treated effluent indicated the inefficiency of treatment processes in their removal. This highlights the potential of these WWTPs in contaminating receiving water sources.