Wastewater exerts toxic effects on plant productivity. Depending on the wastewater composition and the sensitivity of the plant species the effect can vary. The current study was planned to investigate the quality of wastewater taken from sugar and textile industries and their toxic effects on onion (Allium cepa). In this study effects on Allium cepa are evaluated with three replicates. Twenty-four pots were filled with soil. Three concentrations of each wastewater along with control were chosen to investigate the toxicity level of sugar and textile industry wastewater. The concentrations for sugar and industry effluent were chosen: 80% (A1), 90% (A2), and 100% (A3) and for textile industry 80% (B1), 90% (B2), and 100% (B3). Compared to control, treatment with wastewater resulted in root growth inhibition. Chromosome abnormalities were revealed by a genotoxic investigation at various concentrations. The mitotic index decreased and abnormalities in the chromosomes grew as the concentrations rose. As the concentration of wastewater increased, the toxic effects expanded and led to reduction in cortical parenchyma breadth, vascular cylinder diameter, casparian strip and xylem vessels width. Overall, it was discovered that the application of sugar wastewater and wastewater from the textile industry impacted the plant growth negatively. However, the toxicity is more in case of textile wastewater compared to sugar industry wastewater. Textile wastewater was enriched with heavy metals compared to sugar industry wastewater.