The waste generated from cement manufacturing is an important source of heavy metal contamination of groundwater and soil. This study investigated the concentration of toxic metals in the soil of a major cement factory and nearby groundwater. Ecological and carcinogenic risks of the metals were calculated. Potential reproductive toxicity and genotoxic effects of the samples were assessed in sex and somatic cells of male mice using sperm abnormalities and bone marrow micronucleus (MN) assays, respectively. Also, the serum ALP, ALT, AST, Total Testosterone (TT), Luteinizing Hormone (LH), and Follicle Stimulating Hormone (FSH); and liver SOD and CAT activities were measured in the treated mice. Cr, Cu, Ni, Zn, Mn, Cd, and Pb levels in the soil and groundwater exceeded the allowable maximum standard. Ingestion and dermal contact were the most probable routes of human exposure with children having about three times higher probability of exposure to the metals than the adults. Ni, Pb, and Cr presented carcinogenic risks in children and adults. In the MN result, nuclear abnormalities in the studied mice especially micronucleated polychromatic erythrocytes increased significantly (p < 0.05). Compared to the negative control, the ratio of PCE/NCE showed the cytotoxicity of the two samples. Data further showed a significant increase in the serum ALP, AST, and ALT while the liver CAT and SOD activities concomitantly decreased in the exposed mice. Sperm morphology result showed that the samples contained constituents capable of inducing reproductive toxicity in exposed organisms, with alterations to the concentrations of TT, LH, and FSH. Toxic metal constituents of the samples were believed to induce these reported reproductive toxicity and genotoxic effect. These results showed the environmental pollution caused by cement factory and the potential effects the pollutants might have on exposed eukaryotic organisms.