Hydroponic cultivation of fresh produce is gaining popularity worldwide, but few studies have provided a comparative assessment of hydroponic and conventional soil-based vegetables. In this study, we analyzed a series of hazardous chemicals, including 120 pesticides, 18 phthalates (PAEs), and 2 heavy metals (lead and cadmium) in four vegetable commodities (lettuces, celeries, tomatoes, and cucumbers) from hydroponic and conventional soil-based cultivation. Our study showed that at least one pesticide was present in 84% of the conventionally grown samples, whereas only 30% of the hydroponic samples contained detectable pesticide residues. Regarding the total PAE concentrations, there was no significant difference between conventional and hydroponic vegetables. The lead and cadmium residues in conventionally cultivated vegetables were significantly higher than in those produced from hydroponic cultivation. Lead is the primary heavy metal pollutant across all vegetable samples. The hazard index (HI) values of the hydroponic and conventional vegetables were 0.22 and 0.64, respectively. Since both values are below one, the exposure to these hazardous chemicals through consumption of the studied vegetables may not pose a significant health risk. The HI values also suggested that the health risks of eating hydroponic vegetables are lower than for conventional soil-based vegetables.