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Lebanon has been suffering from severe waste crises since the mid-1990s. These problems have been exacerbated by the presence of more than 1.5 million registered displaced Syrian refugees, who are distributed throughout Lebanon. Deir Kanoun Ras El Ain is a southern Lebanese village whose Syrian refugees make up around 11.5 % of the total population. This village possesses significant underground water resources that are used for both domestic and irrigation purposes (1255 hectar). In addition, it has one of the worst dumps in the country, where leachates from medical, industrial, household wastes flow into a canal that runs alongside. Leachates were collected from this dump and from a canal that runs along it at different sites during two seasons. Samples were tested for pH, selected physico-chemical parameters, and bacterial load. The isolated bacteria were identified via 16S rRNA sequencing. Enterobacter, Serratia, Shigella, Citrobacter, Bacilli, Vibrio, Klebsiella, and Escherichia species were among the identified bacteria. Extending along the canal, a significant increase in bacterial count was noticed due to anthropogenic activities rather than due to the dump’s leachates. In conclusion, our results emphasize that immediate actions must be taken to alleviate additional health risks to Lebanese and Syrian Refugees living in the area due to bacterial contamination in canal water used for irrigation and drinking on certain occasions.