Ruppia maritima and Echinodorus amazonicus were prepared in a dehydrated powder form. The characteristics and mechanisms of adsorption of heavy metals were studied under various pH values, reaction times, and heavy metal ion concentrations. The results showed that under different pH and reaction time conditions, heavy metal adsorption was lead > cadmium > zinc > copper. The adsorption of lead increased linearly with the lead concentration. For cadmium, zinc and copper, the adsorption was saturated when metal ion concentration exceeded 200 mg/L. When a Freundlich model was applied, R 2 values for the heavy metal adsorption by the aquatic plants mostly exceeded 0.9. The adsorption of heavy metal ions by these two aquatic plant powders was better explained by the Lagergren second-order equation than the first-order equation. From the Fourier Transform Infrared spectra, there was an adsorption peak at 2,115 cm−1 for R. maritima. The peak shape did not change with metal affiliation except there was a shift of peak wavelength before adsorption. The results indicate that the mechanism of heavy metal adsorption by the two species is not simply on the mono-molecular layer level, and that intra-particulate dispersal is the dominant process. Heavy metal pollution does not affect the basic chemical components, and major substances involved in heavy metal adsorption including carbohydrates, cell wall pectin, and protein functional groups.