The impact of drainage water pollution on the genetic material of  bioindicator Allium cepa L. was assessed by cytogenetic analysis. Allium cepa L. was germinated in three samples of drainage water in addition to the Nile water as a control. Waste water used in this study included agriculture drainage water and liquid industrial wastes resulted from chemical fertilizer industry. This study aimed to investigate the cytological effects of drainage water from different resources on root meristems cells of Allium cepa L. Exposure of onion roots to the waste water showed chromosomal abnormalities which was pollution–dependent. Drainage water induced a variety of chromosomal abnormalities which gradually increased in Kfr El – Sheikh drainage water, Menyet El – Nasr drainage water and industrial waste water, respectively. The drainage water discharged in Menyet El – Nasr center and that discharged from chemical fertilizer industry was effective in forming micronuclei, binucleated cell and disturbance of the spindle fibre apparatus due to high concentrations of chemicals present in these drainage wastes. The toxic chemicals present in drainage water were responsible for the observed genotoxic effects. Laggards, sticky chromosomes, anaphase bridge and fragmented chromosomes being the most frequently seen in all treatments with drainage water. Treatment with drainage water decreased mitotic index and increased the frequency of chromosomal abnormalities compared with the control. To conclude, the untreated drainage water mostly contain toxic chemicals leading to mutagenicity. Based on these findings, the bio monitoring investigation and treatment of drainage water before discharging into the environment are needed. Therefore, mutagenicity/ genotoxicity assays must be considered in water quality monitoring programs to avoid the mutagenic hazards of waste waters.