Coastal recreational waters are continually at risk of fecal contamination, which pose a significant public health concern since fecal material often harbor pathogenic bacteria. Recent reports still indicate high levels of fecal coliform in several areas of Manila Bay. Although quantifying fecal coliform is a standard parameter in water quality monitoring, it does not account for the entire microbial pathogen community in the environment. Characterizing the pathogens present helps in addressing the risks as well as designing preventive strategies to minimize concerns to public health. Moreover, understanding the environmental parameters that influence pathogen loading into the system is important in predicting and preventing pathogen transmission. Traditional techniques in pathogen detection such as culture-based assays, PCR, and microarrays are labor-intensive, unable to detect a majority of pathogens in the natural environment, have sensitivity issues, and rely on the availability of prior data. With the advent of metagenomics, it is now possible to account for the total microbial diversity in a single sample. This study will utilize next-generation sequencing to identify the microbial pathogen community from selected sites in Manila Bay, with focus on pathogenic bacteria, as well as use the microbial community signature for microbial source tracking (MST). Information on microbial diversity will also be correlated with various physico-chemical parameters to determine how these abiotic factors influence the microbial community. The outcome of this research can (1) provide the microbial community composition of samples from Manila Bay, (2) detect and identify pathogenic bacteria which pose risks, (3) determine the parameters as well as pollution sources that influence the pathogenic community, and (4) develop protocols for the monitoring of water quality in Manila Bay and potential pollution sources. This information can lead to more concrete steps in controlling pathogen load into the bay, thus, improving its overall water quality.