A biocidal level of hydrogen peroxide (H2O2), far beyond the natural level, is widely used to control bloom-forming cyanobacteria in freshwater. The extracellular polymeric substance of these cyanobacteria is a key factor in determining the applied H2O2 dosage. The exopolysaccharide (EPS) in the extracellular polymer shows H2O2 scavenging capability. However, the scavenging capabilities of EPSs from other cyanobacteria against biocidal levels of H2O2 as well as their protective roles against cyanobacterial cells are not well known. In this study, we used four nonbloom-forming cyanobacteria as target organisms, two with rich EPS envelopes (EPS-rich strains) and two with thin EPS envelopes (EPS-thin strains), to assess the roles of EPS. It was found that the two EPS-rich strains were much more tolerant to a high dose of exogenous H2O2 than the two EPS-thin strains. The EPSs extracted from the four strains exhibited similar but rapid H2O2 scavenging activity. Additionally, the EPSs from the EPS-rich strains could improve the tolerance of the EPS-thin strains to H2O2 stress, implying potentially nonselective protection against oxidative stress. In addition, all the cell lysates of the four strains showed H2O2 decomposition ability, with the efficiency being slightly different between the two types of strains. This study suggests that cyanobacterial EPS plays a generally crucial role against external strong oxidative stress and may provide a useful reference for the application of H2O2 in environmental management.