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Lebanon is affected by a protracted environmental and solid waste crisis that is threatening the water resources and the public health of its communities. This study is part of a public participatory research project that aims to evaluate the impacts of solid waste disposal practices on water, air, and health in six villages of Lebanon, stigmatized by the presence of a regional landfill. Community mapping enabled the selection and testing of seven springs and three wells in the upstream basin and 11 wells in the lower basin, covering a broad list of chemical, physical, and bacteriological parameters. Two water quality indices (WQ-1 and WQ-2) were used to assess water quality in the study area. The results for the upstream wells and springs showed a significant bacteriological contamination, while the results in the lower wells showed high levels of conductivity, chlorides, and zinc along with the occurrence of organic micropollutants in trace concentrations. The comparison between the experimental data, with the natural background value established in the same area, did not show major differences, except for zinc and bacteriological indicators. The bacteriological contamination is most likely related to sewage infiltration into groundwater at the time of the assessment. Zinc may result from landfill leachate infiltration but also well corrosion. Saltwater intrusion affecting the coastal basin is masking the results for conductivity, chlorides, and sulfates, whereas the presence of small traces of organic micropollutants in the coastal aquifer may be related to leachate infiltration. WQI-1 results, which included bacteriological indicators, showed highly degraded water quality in the C1-C3 inner basin. In contrast, WQI-2, which includes physio-chemical indicators only, showed good water quality, slightly deteriorating in the coastal area, downstream of the Naameh landfill.