Limited freshwater (FW) availability due to climate change and increasing global populations is driving agriculture in arid and semi-arid regions to recycle vast quantities of water for irrigation. However, irrigation with treated wastewater (TWW), which contains dissolved organic matter, salts and microorganisms might alter soil microbial populations, and thus affect soil fertility. We characterized the effects of irrigation with TWW and FW on soil bacterial community composition for three consecutive years. Orchard samples were collected at the end of each of the rainy (winter) and irrigation (summer) season. Community composition, determined by 16S ribosomal DNA amplicon pyrosequencing, was highly similar in soil samples obtained at the end of three consecutive rainy seasons, regardless of irrigation season water quality. However, whereas composition in soil shifted slightly during irrigation seasons by FW irrigation, it was greatly influenced by TWW irrigation. During the irrigation season, a decrease in the relative abundance of Actinobacteria was observed; along with an increase in the relative abundance Gammaproteobacteria within TWW-irrigated soils. The return to the ‘baseline state’ during the rainy season demonstrates that the soil community is not resistant to anthropogenic impact imposed by irrigation water quality, yet is resilient in long term.