Due to its scarcity, wastewater reuse has become an essential element in water resources and agriculture planning and management in arid regions. This research aimed to study the effect of irrigation with diluted wastewater on the yield, water use efficiency (WUE), fecal coliform bacteria count, and toxic metals in relation to the root and the fruit of okra and eggplant crops under surface and subsurface drip irrigation systems. A strip plot design (split block) was used in field crop experiments carried out over two consecutive seasons (2011 and 2012) at an agriculture research station in the Western region of Saudi Arabia. The main plot treatments contained six wastewater qualities and two irrigation systems arranged in strips with subplots of 2 × 3 m each. The results showed no significant difference between the two irrigation systems on the fruit yield/ha and WUE of okra, while in eggplant, the subsurface irrigation showed a significant difference. On the other hand, the root toxic metal (Cd, Cr, Ni, and Pb) concentrations of both crops were significantly higher under the surface irrigation. Conversely, there was no significant difference of toxic metals in fruit under the two irrigation systems, yet the number of fecal coliform bacteria was affected noticeably under the two irrigation systems in both crops. In general, as the percentage of wastewater in the irrigation water increases, the number of bacteria and the concentration of toxic metals increase. However, the rate of increase varies among the six water qualities. More importantly, all detected metal concentrations were less than the cytotoxic concentrations according to WHO/FAO standards.