Cyanobacteria and their toxins (e.g., microcystins) commonly occur in waste stabilization ponds (WSPs), and are a risk to human and ecological health. Although many studies have investigated their removal from batch cultures and drinking water reservoirs, few have been conducted into their removal from WSPs. Hydrogen peroxide (H2O2) has been reported as a benign chemical to decrease cyanobacteria. This study reports on the applicability of the use of H2O2 for the removal of cyanobacteria and microcystins from wastewater. An approach is described which presents an economical and rapid method for determining the appropriate dosage for full-scale application to WSPs. Evidence is presented from full-scale trials that indicate that where H2O2 is added upwind, wind-induced mixing during application is sufficient for treatment of an entire WSP. However, our data also shows that reduction of cyanobacteria is higher in the upper layer of WSPs. This may potentially lead to an overestimation of the overall reduction if only surface samples are considered. As H2O2 significantly decreased the cyanobacterial fraction and microcystin concentrations within days of application, and growth of eukaryote phytoplankton increased, we suggest that H2O2 may be an efficient algicide treatment in WSPs. The longevity of this effect was in the order of three weeks, indicating that repeated application might be necessary to avoid the development of renewed dominance of cyanobacteria. However, such a repeated application needs close monitoring, as, at this stage, the information on the effect on other organisms in full-trials at WSPs is limited. For instance, although recent laboratory experiments suggest that the average doses used in experiments could lead to death of zooplankton within 24 h, this is unlikely to happen in WSPs due to the zooplanktons’ ability to actively avoid unfavourable conditions. In summary, this paper offers WSP operators the possibility to assess the benefit of using H2O2 to rapidly suppress cyanobacterial and microcystin concentrations and hence prevent them from entering the environment.