This study aims to assess the applicability of quantitative PCR (qPCR) for removal studies of adenovirus, coxsackievirus, echovirus and Cryptosporidium by water treatment processes. Bench-scale coagulation jar tests were performed using the enteric viruses and Cryptosporidium. Standard methods (conventional cell-culture methods for the viruses and an immunofluorescence assay (IFA) for Cryptosporidium) were used to compare to qPCR. A significant correlation between microbial removals determined by qPCR and the standard detection methods and an approximate 1:1 correlation were observed for the challenge microorganisms. The results indicated that qPCR could be a satisfactory alternate for microbial removal studies using a relative quantification approach.