Microfluidic quantitative polymerase chain reaction (MFQPCR) and conventional quantitative polymerase chain reaction methods were compared side by side in detecting and quantifying 19 genetic markers associated with Escherichia coli and select bacterial pathogens in algae, beach sand, and water from Lake Michigan. Enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli, Salmonella spp., Campylobacter jejuni, and Clostridium perfringens were among the pathogens tested. Of the pathogenic markers, eaeA that encodes intimin in EPEC was detected in all sample types: water (5%), detached/floating algae (42%), exposed/stranded algae (43%), sand below exposed algae (27%), and nearshore sand with no algae (22%). Other pathogenic markers, however, were detected sporadically. Despite comparable results from the two methods for the genetic markers tested in this study, the MFQPCR method may be superior, with the advantage of detecting and quantifying multiple pathogens simultaneously in environmental matrices.