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Agricultural irrigation with wastewater is common in arid areas but has possible public health and environmental side effects, as effluent may contain pathogens, high level of salts, detergents and toxic metals. In order to ascertain effects of a local textile mill’s wastewater irrigation on soil and subsequently the micro and macroflora, a series of analysis were conducted on soil collected from different sites with regard to pH, EC, organic matter, SO4-2, NO3-1 and exchangeable cations. Soil samples were also determined for total and bio-available metal ions such as Cr+6, Zn+2, Cu+2 and Ni2+. Macroflora of the mill contained high concentration of metal ions. Microbial community identified in the soil samples was different from reference soil. Vesicular arbuscular mycorrhizae (VAM) population associated with Zea mays irrigated by effluent contained 3 ecotypes of VAM, viz., Glomus mossea, Glomus spp., and Acualospora spp. Out of 34 bacterial strains isolated and characterized, dominant genera were Bacillus, Micrococcus and Listeria. Endurance of Cr+6 by Bacillus fumus RH 109 was recorded upto 1000 mg/L, Zn+2 upto 325 mg/L by Pseudomonas stutzeri RH71 and Alcaligenes spp. RH88, while Agrobacterium spp., RH102, Bacillus subtilis RH 96, Bacillus pumilus RH84 and Lactobacillus spp. RH66 tolerated 150 mg/L Ni+2 and 18 bacterial isolates were able to grow un upto 100 mg/L Cu2+. The findings suggest that irrigation with local textile wastewater not only alters the soil chemistry, but also changes bacterial and VAM population in addition to enhancing the intrinsic endurance of these microbes to different metal ions present in their microenvironment. In view of these findings, we recommend monitoring of toxic effects of wastewaters and conclude that such irrigation practices should be carried out only after treatment of wastewater.