Bacteroides spp. has gained substantial interest among the suggested potential candidates for alternative faecal indicators for untreated recreational waters by the US EPA. Interest in Bacteroides as a faecal indicator is based upon the relative abundance of selected members of the Bacteroides genus in the human colon and human faeces. In this study, we developed a real-time PCR detection system based on gyrase B subunit genes (gyrB) specific to Bacteroides fragilis. The gryB-based method was compared with previously described 16S rRNA-based real-time qPCR methods and evaluated for specificity, sensitivity and robustness in detecting B. fragilis from untreated recreational water impacted by human and non-human faecal sources. The new gyrB-based system only detected B. fragilis, whereas the 16S rRNA-based methods generated cross-amplifications with other Bacteroides and Prevotella species. We used a procedure of prefiltration, filtration, sonication and DNA concentration in order to improve the DNA extraction efficiency and the sensitivity of the real-time PCR while removing interference. The amplification and sequencing of PCR products generated by the gyrB-based method confirmed that gyrB-amplified sequences only contained B. fragilis. This rapid method is useful for quantifying faecal contamination and may assist beach and watershed managers in elucidating possible contamination sources.