Domestic rainwater harvesting (tank water) systems were screened for the presence of a panel of microbial source tracking (MST) markers and traditional indicator organisms. The indicator organisms were enumerated utilizing traditional culture-based methods, while the MST markers were quantified by quantitative PCR (qPCR). The indicators Escherichia coli (E. coli) and enterococci were also quantified using qPCR. Correlations and concurrence between these parameters were then investigated to determine which markers could be utilized to supplement traditional indicator analysis. Quantitative PCR analysis indicated that Bacteroides HF183, adenovirus, Lachnospiraceae and E. coli were detected and quantifiable in 100% of the tank water samples collected throughout the sampling period, while human mitochondrial DNA (mtDNA) was quantifiable in 90% of the tank water samples and Bifidobacterium adolescentis (B. adolescentis) and enterococci were quantifiable in 67% of the tank water samples, respectively. Significant positive correlations were recorded for Lachnospiraceae versus heterotrophic bacteria (p = 0.000), adenovirus versus E. coli (culturing) (p = 0.000) and heterotrophic bacteria (p = 0.024), the HF183 marker versus E. coli (qPCR) (p = 0.024) and B. adolescentis versus fecal coliforms (p = 0.037). In addition, 100% concurrence was observed for the HF183 marker, adenovirus and Lachnospiraceae versus E. coli (qPCR), enterococci (qPCR) and heterotrophic bacteria, amongst others. Based on the correlations and the concurrence analysis, the HF183 marker, Lachnospiraceae and adenovirus may be utilized to supplement indicator organism analysis for the monitoring of harvested rainwater quality.