As the demand for fish increases, the amount of wastewater generated from fishponds is also increasing with potential environmental and public health effects from their indiscriminate disposal. This study aimed at comparative analyses of the physicochemical and heavy metal constituents and potential DNA damage by wastewaters from natural and artificial fishponds using Allium cepa assay. A. cepa were grown on 3.13, 6.25, 12.5, 25.0, and 50.0% (v/v; wastewater/tap water) concentrations of each wastewater. At 48 and 72 h, respectively, genotoxic and root growth inhibition analyses were carried out on the exposed onions. The onion root tips exposed to wastewaters showed a significant (P < 0.05) inhibition of root growth and cell division in a concentration-dependent manner. Additionally, chromosomal abnormalities like spindle disturbances, sticky chromosomes, micronucleus, bridges, and binucleated cells were observed in the exposed onions and their induction was higher significantly relative to the negative control. Generally, wastewater from the natural fishpond caused higher chromosomal aberrations than the wastewater from artificial fishpond. It is our belief that the cytotoxicity and genotoxicity observed in the onions were primarily caused by heavy metals like Cr, Cd, Fe, Pb, Cu, and Zn found in the wastewaters. These metals also showed a significant carcinogenic and non-carcinogenic risks in children and adults with Cd as the highest contributor to these detrimental risks. Ingestion route was the major exposure route to the toxic metals in these wastewaters. Wastewater from the natural fishpond showed a higher health risk than the wastewater from the artificial fishpond. These findings suggest that the wastewaters from natural and artificial fishpond contain compounds that might induce cytogenotoxicity in exposed organisms.