In this article, we have examined toxicity of nanostructures such as flower-like ZnO capped with starch, spherical uncapped ZnO and spherical CdS on aquatic plant Hydrilla verticillata, which has not done before. Hydrilla plant was exposed by these nanoparticles at a concentration of 400 mg/L for 7 days and changes in the biochemical parameters such as catalase activity, chlorophyll content and protein content were observed. It was perceived that spherical CdS nanoparticles were more toxic than the corresponding ZnO nanoparticles since there was a decrease in chlorophyll content and increase in catalase activity. This effort upsurge an interest in understanding the hazards of nanomaterials and their risk, which poses an impact on our environment and how they can be monitored via simple biochemical assays on plant systems.