This study investigates the role of secondary metabolites in the phytoremediation of cadmium-contaminated water using Pontederia parviflora and Salvinia auriculata. Unlike previous studies, which primarily focus on the physical removal of heavy metals by plants, our research explores the biochemical interactions between these plants secondary metabolites and cadmium ions. We employed liquid chromatography-diode array detector-mass spectrometry (LC-DAD-MS) to analyze the chemical composition of the plant extracts and assessed the impact of these metabolites on cadmium accumulation and removal efficiency. Our findings reveal that the removal of secondary metabolites from plant biomass did not significantly alter the cadmium removal efficiency, challenging the commonly held belief that these metabolites play a central role in heavy metal sequestration. Additionally, our results indicate that cadmium uptake is more closely associated with structural components of plant tissues rather than the presence of specific secondary metabolites. This study provides new insights into the mechanisms of phytoremediation and suggests that the optimization of plant selection for remediation efforts should focus on the structural properties of plant tissues rather than secondary metabolite content.