Available domestic water in many communities in Nigeria is increasingly polluted on a daily basis. A major issue of national interest is how these polluted drinking water sources could be fully assessed and mitigated. In this study, mycofiltrated domestic water samples obtained from hand-dug wells and boreholes in six rural communities in Ughelli South Local Government Area of Delta State, Nigeria were evaluated for potential cyto-genotoxicity using the Allium cepa bioassay. Data obtained from physicochemical analysis after a 24- hour mycofiltration treatment of the water samples revealed significant (p < 0.05) reduction/total elimination of heavy metals and microbial load in the samples. Results obtained from the 96-hour macroscopic evaluation of A. cepa showed that compared to onions grown in untreated samples, significant (p < 0.05) reduction in root growth inhibition occurred in bulbs cultivated in mycofiltrated samples. Root tips of A. cepa processed for cytological studies by the aceto-orcein squash technique after exposure to the water samples for 48 hours also showed significant (p < 0.05) reduction in chromosomal aberrations in onion bulbs grown in mycofiltrated samples. These findings show that mycofiltration technique is an efficient and affordable technology for toxicity reduction in drinking water sources available for rural dwellers in developing countries.