Background: Leafy greens, particularly romaine lettuce, are often associated with outbreaks due to their susceptibility to contamination from various environmental sources. This study aimed to evaluate the presence of E. coli, Salmonella, copper, nickel, zinc, and manganese in irrigation water, lettuce leaves, and agricultural soil in the Litani River Basin (LRB), Lebanon. Method: Samples were collected from five demonstration plots employing different agricultural practices. Heavy metal concentrations were determined using atomic absorption spectrometry, while E. coli and Salmonella testing were conducted through conventional culturing techniques. The impact of E. coli contamination on seed germination and the interaction effects between E. coli and heavy metals were also examined. The study also compared the effectiveness of various irrigation systems in reducing bacterial contamination. Results: The results demonstrated that contamination levels varied significantly across the plots and irrigation types. This variation underscores the necessity of site-specific mitigation strategies to enhance food safety. Our findings highlight the importance of selecting appropriate irrigation methods and implementing tailored agricultural practices to minimize the risk of contamination. Conclusion: This research provides valuable insights for optimizing agricultural practices in the LRB to ensure food safety and environmental sustainability.