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.Fecal pollution has negative impacts from both environmental and economic perspectives. The presence of traditional fecal indicator bacteria (FIB), namely, Escherichia coli and Enterococcus, is the standard by which the extent of fecal contamination and potential health hazard is currently assessed for recreational waters. Determining the presence of FIB is a relatively easy task, but determining the source(s) is a considerably more complex problem. Molecular methods based on the identification of 16S rRNA gene markers of fecal Bacteroidales have been successfully applied to delineate the sources of fecal pollution based on differences in host species intestinal community compositions (9,20,34). Determination of the mere presence of different sources of fecal pollution by using host-specific Bacteroidales markers was a significant advance for water quality analysis. The next problem that presented itself was quantifying the relative contributions of fecal pollution from respective sources. Since the first Bacteroidales hostspecific molecular marker detection systems were published, studies have followed describing quantitative PCR (qPCR) methods for quantifying the abundance of specific markers (15,21,25,28) in natural samples. Although enumeration of the specific markers is currently possible, it is clear that host-specific marker quantities in natural waters do not d...