Using treated wastewater (TWW) for irrigation could alleviate potable water (PW) stress and provide food security in arid environments. However, TWW irrigation could present a considerable health risk especially when used for vegetables that are eaten raw. Furthermore, the effect of TWW irrigation on soil health is still debated because this water contains dissolved organic matter, salts, and microorganisms including pathogens. While risks of direct application of TWW on plant material are quite well understood, the importance of soil type to enhance or attenuate the risk of pathogens’ contamination remains unclear. Moreover, under field conditions, targeting and tracking of pathogens in TWW irrigated soils and crops have not been extensively studied. Therefore, to avoid contamination due to TWW irrigation, health authorities have mandated the use of barriers, such as drip irrigation and plastic mulch, to segregate the irrigation water from the crops. Although barriers are mandated, it is not clear whether they prevent contamination of crops. We hypothesized that microbial contamination of soil types and crops are not linked to the irrigation regime and that no differences will be detected between soil and crops irrigated with PW or TWW. In addition, We hypothesized that TWW barriers and soil types will alter the soil microbial and pathogens composition and diversity. To explore our hypotheses, an experimental field site was established in Neve Ya’ar Agricultural Research Center, with field experiments at which cucumber (Cucumis sativus) and melons (C. melo) were cultivated with secondary TWW during two cultivation seasons. Our research aimed to: (i) Characterize the fate of indicators and pathogens in soil types differing in their particle size fractions (i.e., sand, silt and clay) under TWW irrigation (ii) Study the effect of different irrigation approaches, namely surface and subsurface drip irrigation, and the application of soil plastic mulch on indicators and pathogens in TWW irrigated soil and crops (iii) Track the source of fecal contamination in the soil and crops (iv) Explore the effect of irrigation, TWW barriers and soil types, on soil microbial diversity and community composition over time. We compared water qualities (TWW and PW), soil types (clay, loam and loamy-sand), soil treatments (drip irrigation, subsurface drip irrigation and plastic cover) and crops (cucumber and melon). Over 700 samples of water, soil and crop (surface and tissue) were tested for their physico-chemical and microbial characteristics as well as the presence, abundance and source of pathogens, using culture dependent and independent techniques.