Cyanobacterial blooms compromise water quality worldwide, demanding nutrient input control. However, once established, other strategies are necessary to control the growth of cyanobacteria. Oxidation processes such as hydrogen peroxide (H2O2) offer a potential solution; however, research on planktonic community recovery post-H2O2 exposure is limited. Here, we investigated the impact of the addition of H2O2 alone at various concentrations (1, 10, and 100 mg/L) on the natural phytoplankton and bacterioplankton communities of a eutrophic reservoir over 21 days under laboratory conditions. We aimed to evaluate the differential susceptibility of cyanobacteria and green algae, possible phytoplankton regrowth, changes in bacterioplankton composition and the effect of residual H2O2 or its byproducts on organisms at different trophic levels. Initially, cyanobacteria (mainly Microcystis and Cyanobium) were the main contributors to chlorophyll (Chl) concentrations, followed by green algae. Within 7 days, the phytoplankton abundance decreased under all conditions, with pronounced effects occurring in the H2O2 treatments within the first 48 hours. H2O2 exposure led to residual Chl concentrations for cyanobacteria and green algae, and after fresh culture medium addition, green algae, but not cyanobacteria, were able to regrow in the <10 mg/L treatment. At lower H2O2 concentrations, Microcystis, Cyanobium, Limnothrix, and Planktothrix resisted, while at higher concentrations, Cyanobium and Mastigocladopsis persisted. In the bacterioplankton community, H2O2 addition led to a greater abundance of taxa from the hgcI clade, Comamonadaceae family, Craurococcus-Caldovatus and Staphylococcus. Ecotoxicological assays revealed transient effects of H2O2 on Daphnia similis survival, while Danio rerio remained unaffected. Our findings demonstrate that, compared with cyanobacteria, green algae exhibit greater resistance and resilience to H2O2, with transient effects on zooplankton at concentrations up to 10 mg/L. This research underscores the complexity of managing cyanobacterial blooms and emphasizes the need for comprehensive strategies considering ecological impacts.