Recently, management of soil irrigated with low-quality water has become necessary to have a healthy crop. This research work aims to design the best management practices (BMP) to minimize drainage water hazards in the soil ecosystems. Based on the source of irrigation water, a column experiment was implemented on three soil samples that collected from three governorate in Egypt. The subsistence of enteric pathogens in soil irrigated with three types of low-quality water either sole sewage effluent (Giza) or a mix of drainage and industrial effluent (Kafr-el-sheikh) or drainage effluent (Sinai) was monitored periodically for 90 days. The trailed soils were divided as: non inoculated cultivated (C) or inoculated cultivated with sole phosphate dissolving bacteria (T1) or Acidithiobacillus sp. (T2) or with a combination of both microorganisms (T3). Three common hyperaccumulator plants (Brassica napus, Plantago psyllium, and Plantago major) were cultivated separately in cultivated, inoculated soil trials in comparison to non-cultivated, non-inoculated control treatments (NC). Results section illustrates the removal pattern of fecal coliforms and Salmonella sp. in the trailed soil ecosystems, in response to different treatments during 90 days of experimental monitoring. The trailed remediation amendments, either in the single or combined application, followed by phytoremediation with three different phytoremediation plants, exhibited a positive effect in diminishing pathogenic bacteria in the three tested soil ecosystems, yet at varying degrees. The study concludes that, applied mixture of all treatments represented by choice of Plantago psyllium (as best phytoremediator plant) and combination of two remeditative bacterial inoculums (Acidithiobacillus and phosphate dissolving bacteria) in contaminated soil was selected as the BMP among the other applied treatments.