This study assessed the cytogenotoxicity of water samples obtained at the discharge site and about 1.5 km downstream of the discharge site of a textile factory along Challawa River, Kano, Nigeria. After physicochemical and microbial characterizations, water samples were used to grow 20 Allium cepa bulbs divided into two equal groups for 72 hrs. A control group was similarly conducted, but was grown over deionized water. Root-tips of the bulbs were then examined for chromosomal aberrations. Physicochemical analysis showed that the levels of Ca, Cd, Cr, Pb, DO, BOD, COD, turbidity, and nitrate in both water samples were not within WHO standards. Only the bacterial loads of samples from 1.5 km distance were abnormal in the microbial analysis. A significant (p<0.05) reduction in mitotic index and bi-nucleated cells, sticky and vagrant chromosomes were observed in the treated bulbs. These findings showed that the water samples could be toxic.