Saudi Arabia produces a majority of its fruits and vegetables locally in small-scale production farms. These farms utilize groundwater as the main source of irrigation water. The water-regulating authorities in Saudi Arabia rely on traditional culturing methods to monitor coliforms as indicators of microbial contamination. These methods are time-consuming, do not address the sources of contamination, and do not permit assessment on the associated health risk. To address these knowledge gaps, the study investigates the sources of contamination in eight wells northeast of Mecca, Saudi Arabia. The study focuses on the potential impact on groundwater quality due to a nearby chicken farm and urban runoffs from human residential areas. Besides performing conventional methods to determine nutrient content and to enumerate coliforms, quantitative PCR using four host-associated primer sets were used to distinguish microbial contamination from humans and livestock. High-throughput sequencing was also performed to determine the relative abundance of several genera associated with opportunistic pathogens. Bacterial isolates were cultivated from the vegetable samples harvested from these farms, and were characterized for their phylogenetic identities. Lastly, the study collates the information to perform quantitative microbial risk assessment due to ingesting antibiotic-resistant Listeria monocytogenes, Pseudomonas aeruginosa and Enterococcus faecalis in these vegetable samples.