The frequent occurrence of cyanobacterial blooms, caused by the eutrophication of water bodies, has triggered several ecological issues. Metal-controlled cyanobacteria are resulting in a series of secondary environmental problems and thus limiting environmental sustainability. Whether there is a more environmentally friendly way to replace metals in the removal of cyanobacteria is still unclear. To explore whether common heavy metals inhibit algal growth and whether Eucalyptus leaves (EL) can replace heavy metal ions in controlling algae outbreaks, here, we add Fe³⁺, Al³⁺, 3 mol/L of zinc (Zn₃), 10 mol/L zinc (Zn₁₀), and EL to a medium containing Cyanobacteria. We determine the medium’s color (456 nm), UV (254 nm), chlorophyll a, turbidity, temperature, pH, total dissolved solids, conductivity, and blue-green algae (BGA) at days 1, 4, 7, 11, 14, 19, and 21. We find that Fe³⁺, Al³⁺, Zn₃, Zn₁₀, and EL can inhibit chlorophyll synthesis, thereby impeding algae biomass growth due to metal ions’ disruption of the chlorophyll structure. The toxicity of Zn²⁺ may be higher than that of Fe³⁺ and Al³⁺ since it can completely destroy the structure of chlorophyll a. The damage of Zn (10) to chlorophyll a is stronger than that of Zn (3), indicating that high concentrations of metals have a stronger inhibitory effect on algae. The toxicity of EL to algae is lower than that of other metals, but it can significantly inhibit the growth of algae. We suggest the use of Eucalyptus leaves to inhibit algal growth in eutrophic water bodies. Our results provide a scientific basis for an environmentally friendly approach to controlling cyanobacteria outbreaks.