Municipal wastewaters may contain a variety of genotoxic pollutants that are discharged into rivers and causing deterioration of the environment in downstream reaches. The present study evaluates the hazardous effects of untreated municipal wastewater discharge from the city of Bahir Dar to the head of the Blue Nile River. This was done by collecting wastewater samples from the upper, middle and lower sites of the stream and characterizing its physicochemical qualities. In all cases, tap water was taken as a control and the wastewater qualities were significantly varied among the studied sites. The highest values of EC, TDS, COD, etc. were found at the middle site. Further, the wastewater showed significant differences in terms of cytotoxicity (in root number, root length, mitotic index) and genotoxicity (chromosomal aberrations) in Allium cepa tests after three days of growth at (0, 25, 50, 75 and 100 ml) dilution values of wastewater. The cytotoxic effects of wastewater were significantly varied at different treatment values and collection sites of the stream. The mitotic index was reduced to 1.80 ± 0.03 from 12.59 ± 0.28, 1.26 ± 0.02 from 12.78 ± 0.38 and 2.05 ± 0.04 from 12.81 ± 0.19 at 100 ml of wastewater compared to the control at the upper, middle and lower sites respectively. The EC50 values for root growth inhibition followed the order middle < upper < lower, indicating greater toxicity of a middle site. Moreover, the wastewater incurred significantly more genotoxic effects on root tip cells in comparison to the control and also varied among sampling sites. Most recorded abnormalities were anaphase bridges, chromosome fragments, c-mitosis, binucleated and micronucleated cells. Thus untreated wastewater discharges have a potential threat to the water ecosystem and public health as the river is used for different purposes by downstream societies.