Contamination of recreational waters with fecal waste, indicated by the presence of enterococci, can have consequences for human and ecosystem health. The difficulty in determining the extent and origin of fecal pollution in dynamic estuarine systems is compounded by contributions from sources including septic tanks and agricultural runoff. This study investigated fecal pollution at five sites with variable hydrological conditions in the St. Lucie Estuary and Indian River Lagoon. The distribution and occurrence of enterococci was assessed using traditional cultivation. A human-associated microbial source tracking assay was validated and applied in these estuaries using qPCR. Results demonstrated a correlation between enterococci concentrations, rainfall, and salinity. The human-associated assay was sensitive and specific in the lab; however, human fecal pollution was not detected in the field even though samples contained high levels of enterococci. This study highlights the importance of expanding the range of water quality assessment. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection