Abstract. Cyanobacteria and cyanotoxins are a risk to human and ecological health, and a hindrance to biological wastewater treatment. This study investigated the use of hydrogen peroxide (H₂O₂) for the removal of cyanobacteria and cyanotoxins from within waste stabilization ponds (WSPs). The daily dynamics of cyanobacteria and microcystins (commonly occurring cyanotoxins) were examined following the addition of H₂O₂ to wastewater within both the laboratory and at the full scale within a maturation WSP, the final pond in a wastewater treatment plant. Hydrogen peroxide treatment at concentrations ≥ 0.1 mg H₂O₂ μg⁻¹ total phytoplankton chlorophyll a led to the lysis of cyanobacteria, in turn releasing intracellular microcystins to the dissolved state. In the full-scale trial, dissolved microcystins were then degraded to negligible concentrations by H₂O₂ and environmental processes within five days. A shift in the phytoplankton assemblage towards beneficial Chlorophyta species was also observed within days of H₂O₂ addition. However, within weeks, the Chlorophyta population was significantly reduced by the re-establishment of toxic cyanobacterial species. This re-establishment was likely due to the inflow of cyanobacteria from ponds earlier in the treatment train, suggesting that whilst H₂O₂ may be a suitable short-term management technique, it must be coupled with control over inflows if it is to improve WSP performance in the longer term.