The use of polluted water to irrigate is an increasing problem in the developing world. Lebanon is a case in point, with heavily polluted irrigation waters, particularly in the Litani River Basin. This study evaluated the potential health risks of irrigating vegetables (radishes, parsley, onions, and lettuce) using three water sources (groundwater, river water, and treated wastewater) and three irrigation methods (drip, sprinkler, and surface) over two growing seasons in 2019 and 2020. Water, crop, and soil samples were analyzed for physicochemical parameters, pathogens, and metals (Cu, Cd, Ni, Cr, and Zn). In addition, the bioaccumulation factor, estimated dietary intakes, health risk index, and target hazard quotients were calculated to assess the health risk associated with metal contamination. The study showed that, for water with less than 2 log E. coli CFU/100 mL, no pathogens (Escherichia coli, salmonella, parasite eggs) were detected in irrigated vegetables, irrespective of the irrigation method. With over 2 log E. coli CFU/100 mL in the water, 8.33% of the sprinkler-and surface-irrigated vegetables, and 2.78% of the drip-irrigated root crops (radishes and onions), showed some degree of parasitic contamination. E. coli appeared only on root crops when irrigated with water having over 3 log CFU/100 mL. The concentrations of most metals were significantly lower than the safe limits of the FAO/WHO of the Food Standards Programme Codex, except for zinc and chromium. The trends in the bioaccumulation factor and the estimated dietary intakes of metals were in the order of Cu < Cd < Ni < Cr < Zn. The target hazard quotient values for all metals were lower than 1.0. Under trial conditions, the adoption of drip irrigation with water with less than 3 log E. coli CFU/100 mL proved to be safe, even for vegetables consumed raw, except for root crops such as onions and radishes that should not be irrigated with water having over 2 log E. coli CFU/100 mL. Treated wastewater had no adverse effect on vegetable quality compared to vegetables irrigated with other water sources. These results support efforts to update the Lebanese standards for water reuse in agriculture; standards proposed in 2011 by the FAO, and currently being reviewed by the Lebanese Institution of Standards. This research will inform a sustainable water management policy aimed at protecting the Litani River watershed by monitoring water quality.