Bacteroidales are attractive as water quality indicators because of their potential to discern sources of fecal pollution, and it is presumed that these bacteria do not multiply outside their host organisms. The persistence of a fecal Bacteroidales marker was monitored over 14 days in river water microcosms that varied in temperature from 10°C to 30°C and salinity from 0‰ to 30‰ by quantitative PCR (qPCR). Decay rates were estimated and compared to the results of other studies examining the survival and persistence of Bacteroidales markers by converting decay rates from other studies to a common decay rate unit. The log-linear decay rates estimated in this work ranged from -0.18 to -1.31 ln(C(T)/C(0)) day(-1), where C(T) is the threshold cycle and C(0) is the concentration of cells at time zero, which is comparable to findings in previous studies. Salinity had a positive effect on Bacteroidales marker persistence, while decay was more rapid at higher temperatures. Comparison of 16S rRNA gene clone libraries generated from microcosm samples indicated that most of the operational taxonomic unit (OTU) and phylogenetic diversity was found within samples and not between samples, indicating at least qualitatively that diverse lineages persist and likely have similar survival characteristics under most of the conditions examined. It was noted that the samples at higher salinities also had the smallest amount of diversity between samples as well as the lowest decay rates. This research also highlights the need for a repository of raw survival and persistence data if more sophisticated models of decay are to be employed and compared between different studies.