In this study, we selected the aquatic plant Hydrilla verticillata as our specimen and cultured it in clean river sand and water in order to study the influence of five separate concentration levels of Cd²⁺ or Cu²⁺ on the plant. Effects of the stress on the plant were identified, and we recorded parameters such as height, biomass, chlorophyll content, and survival ratios of H. verticillata, as well as the effects of fluorescence parameters such as minimal fluorescence (Fo), maximal fluorescence (Fm), PS II maximum quantum yield (QY_max), degree of PSⅡ reaction centers closed under stable state (1-Qp_Lss), non-photochemical quenching under stable state (NPQ_Lss), and fluorescence images of H. verticillata leaves. We also separately studied the variation characteristics of each parameter of H. verticillata under the stress of increasing Cd²⁺ or Cu²⁺ concentrations. We found that the height of H. verticillata decreased significantly under the different levels of pollution stress by the heavy metal Cd²⁺. This indicated that Cd²⁺ pollution may damage the bundle structure of H. verticillata. There were no significant effects on the fresh weight of H. verticillata under the stress of either Cd²⁺ or Cu²⁺ pollution, and this may be related to the high content of free water in aquatic plants. Dry weight of H. verticillata decreased significantly when the plants were exposed to Cd²⁺ or Cu²⁺ pollution. Effect of Cu²⁺ pollution on the dry weight of H. verticillata was far more prominent than that of Cd²⁺ pollution. All chlorophyll values decreased significantly when the plants were subjected to Cd²⁺ or Cu²⁺ pollution, and we found that the effect of Cu²⁺ pollution was greater than that of Cd²⁺ pollution. This suggested that the toxicity of Cu²⁺ against H. verticillata chloroplasts is greater than that of Cd²⁺. The chlorophyll fluorescence parameters (Fo, Fm, and QY_max) of H. verticillata under Cd²⁺ or Cd²⁺ stress were significantly lower than those of the control groups; however, the values of (1-Qp_Lss) increased, and the values of NPQ_Lss first increased and then decreased as the concentrations of the heavy metals increased. The different values for the physiological parameters, fluorescence parameters, and imaging characteristics indicated that the influence of Cd²⁺ on H. verticillata was greater than that of Cu²⁺ when the same concentrations of the two different heavy metals were used. When Cu²⁺ concentration was lower than 1 mg/L in the water environment, photosynthetic activities of H. verticillata under Cu²⁺ stress were almost normal. This means that H. verticillata could be used to restore a water environment with a low Cu²⁺ concentration. H. verticillata cannot survive for a long time in a water environment contaminated with Cd²⁺ or if Cu²⁺ concentrations reach or exceed 3 mg/L. This means that H. verticillata could be used as an indicator species for water contaminated with Cd²⁺.