Little is known about the magnitude of microbial pollutant loads to rivers from non-point sources such as sewer overflows, sewer exfiltration, or open defecation at transient encampments. This thesis aimed to provide insight about the concentrations and loadings of traditional fecal indicator bacteria (FIB) groups (Escherichia coli and enterococci) and two human-associated microbial source tracking (MST) markers, HF183 Bacteroides (HF183) and pepper mild mottle virus (PMMoV) from these types of non-point sources. Three experiments were performed: 1) a simulated sewer overflow/exfiltration experiment to evaluate the persistence and leaching rates for E. coli, enterococci, HF183, and PMMoV from soil spiked with sewage; 2) a simulated runoff experiment from sites within homeless encampments with evidence of open defecation to evaluate the concentrations of E. coli, enterococci, HF183, and PMMoV leaching from the soils; and 3) analysis of samples collected from a river during two rain events to evaluate the concentrations of E. coli, enterococci, HF183, PMMoV, and bacterial and viral waterborne pathogens (Campylobacter coli, Campylobacter jejuni, norovirus genogroup I, and hepatitis A virus) throughout the duration of the storm. For the simulated sewer overflow/exfiltration experiment, the first order decay rates for HF183 and PMMoV were found to be 0.029/day and 0.004/day, respectively, indicating that the PMMoV marker is more persistent than the HF183 marker in the environment. For the simulated runoff experiment, PMMoV was also detected in the runoff water from all seven open defecation sites analyzed for this marker in the simulated runoff experiment, while HF183 was only detected in the runoff water from one of nine open defecation sites analyzed for this marker at a concentration about an order of magnitude below the lowest concentration of PMMoV. Concentrations of HF183 in river samples during rain events correlated with concentrations of bacterial pathogens, while concentrations of PMMoV correlated with the concentration of viral pathogen, suggesting similarities regarding the fate and transport mechanisms. The findings from this study indicate that the use of HF183 in conjunction with a viral MST marker such as PMMoV will generate a more thorough understanding about the sources of human fecal contamination to water bodies.