Microbial pathogens and indicators have contributed to major part of water quality degradation in the United States. Located in the northwestern New Jersey, the Musconetcong River has been included in the New Jersey Impaired Waters List or the 303(d) List due to high concentrations of fecal indicator bacteria. Hence, a Total Maximum Daily Load plan was established to address microbial water quality issues in the watershed. The objectives of this study were to assess the current status of microbial water quality and to determine potential sources of fecal contamination in the Musconetcong River Watershed using microbial source tracking techniques. Fifteen sampling events in total were carried out at nine sites throughout the Musconetcong River Watershed in August 2016, July and August 2017. E. coli enumeration was performed to determine the possible presence of fecal contaminations. Microbial source tracking techniques, specifically Canada goose, cow, deer, horse, and human-specific molecular markers, were used for real-time polymerase chain reaction (qPCR) analysis in order to identify and quantify potential sources of fecal contamination. The results indicated that E. coli was found present at all nine study sites. Two of the nine sites violated the New Jersey Surface Water Quality Standards in August 2016, while all of the nine sites exceeded the standards in both July and August 2017. Water temperature, dissolved oxygen (DO), and specific conductance at the study sites ranged from 13.5？C to 25.3？C, from 7.7 mg/L to 13.0 mg/L, and 278.5 μS/cm to 1335.0 μS/cm, respectively, at the time of sample collection. E. coli counts were found to be negatively correlated with temperature and specific conductance (p < 0.05) but positively correlated with dissolved oxygen, accumulated rainfall within 1 day, rainfall within 2 days, and rainfall within 3 days (p < 0.05). Higher percentage of presence of human, Canada goose and deer markers were observed at all fifteen sampling events indicating human and wildlife were the two major sources of fecal contaminations in the Musconetcong River Watershed. The study suggested applying restoration measures to reduce fecal contaminations from anthropogenic and wildlife sources in order to improve microbial water quality of the Musconetcong River. However, more frequent and strategic sampling plan is recommended to supply more comprehensive data to aid in future planning of best management efforts on controlling fecal contaminations.
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