Global context of water scarcity triggers the reuse of reclaimed wastewater. This practice, although advantageous, presents risks of pathogens dissemination through wastewater and a modification of soil microorganisms. To date, contradictory results have been published about the influence of these practices on soil microbial communities. A selection of microorganisms involved in the transformation of nitrogenous compounds is often observed. In addition, the persistence of pathogenic microorganisms in water and soil after irrigation with reclaimed wastewater seems affected by plant species and pathogen loads. To resolve the discrepancies observed between studies, a gradient of water qualities with different pathogen loads and nutrients concentration was used during irrigation. The soils (loamy clay soil composition) were, indeed, irrigated with four different water qualities. In order to increase microbiological and physicochemical qualities the following treatment levels were used: raw wastewater, treated wastewater with aerated planted filter, treated wastewater with membrane bioreactor and drinking water. Lettuce crops were selected to monitor the evolution of the microbial community and the fate of microbial contaminants in the soil. Three soil sampling locations were chosen to evaluate the impact of irrigation practice on plant: soil without plants, soil at vicinity to root system and soil tightly bound to root system. Our results show that soil microbial community structures differed over time when exposed to different water qualities. Irrigation with raw wastewater has the most marked effect compared to treated wastewater. Soils irrigated with drinking water and treated wastewaters could not be distinguished based on microbial community structure and pathogens persistence. Overall, our results show an adaptation of soil microbial communities to the disturbance undergone by irrigation with treated wastewater. Moreover, it has been shown that pathogenic microorganisms have a low persistence in the soil which contributes to minimize sanitary risks of wastewater reuse.