State-approved membrane filtration (MF) techniques for water quality assessments were contrasted with metagenomic shotgun sequencing (MSS) protocols to evaluate their efficacy in providing precise health-risk indices for surface waters. Using MSS, the relative numerical abundance of pathogenic bacteria, virulence and antibiotic resistance genes revealed the status and potential pollution sources in samples studied. Traditional culture methods (TCM) showed possible fecal contamination, while MSS clearly distinguished between fecal and environmental bacteria contamination sources, and pinpointed actual risks from pathogens. RNA MSS to detect all viable microorganisms and qPCR of fecal biomarkers were used to assess the possible environmental risk between runoff drainage canals and a swamp area with no anthropogenic impact. Results revealed higher levels of pathogenic bacteria, viruses, and virulence and antibiotic resistance genes in the canal samples. The data underscore the potential utility of MSS in precision risk assessment for public and biodiversity health and tracking of environmental microbiome shifts by field managers and policy makers. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection