A comparative study was carried out to evaluate the effects of two water irrigation sources on the quality and microbiological safety of tomato plants and fruit, and on the microbiological soil properties: irrigation with groundwater (GW) and with treated agro-industrial wastewater (TW). In a field experiment in southern Italy (Apulia region), the physico-chemical characteristics of the irrigation waters and the fruit quality parameters were determined. Escherichia coli, fecal Enterococci and Salmonella spp. were also monitored in the irrigation waters, tomato plant and fruit, and root-zone soil. Bacteriological analysis for total heterotrophic counts (THCs) were determined for plant, fruit, and soil samples. The irrigation water source did not significantly affect yield quantitative traits. However, with GW, the marketable fruit yield was higher than with TW (∼82 vs. ∼79Mgha−1, respectively). For both irrigation treatments, the most important qualitative parameters that characterize the processing tomato fruit (i.e., dry matter content, pH, soluble solid content, color parameters) were in agreement with reports in the literature. For the microbiological results, the mean levels of E. coli and fecal Enterococci were 4408 and 3804CFU 100ml−1, respectively, for TW (above the Italian guidelines for TW re-use). For the tomato plant and fruit, no E. coli isolated in either, and fecal coliforms and THC were not influenced by the irrigation waters (P>0.05). Total bacterial enumeration by quantitative PCR was lower in soil irrigated with GW, than TW (3.69 vs. 4.02, ×106, respectively). Moreover, soil microbial community patterns substantially differed between the two water treatments. These data show that while fecal indicators are not affected, the community composition and dynamics of the whole bacterial population in soil is influenced by the different qualities of these waters used for irrigation