Toxin-producing cyanobacteria constitute a serious threat to human and environmental health. It is thus essential that an effective treatment guarantees the removal of cyanobacteria from wastewater before its inclusion in water recycling or environmental flow. Hydrogen peroxide (H2O2) has been shown to induce cyanobacterial decay in laboratory cultures. However, its application for the removal of cyanobacteria from wastewater treatment ponds under environmental conditions has not been investigated. To examine the effects of environmental factors, field trials were performed at both the mesocosm and full-scale levels. The mesocosm trial was completed under field conditions of incident radiation, with various H2O2 concentrations. A concentration of 1.1×10−4 gH2O2/μg chl-a resulted in a 32% decrease in cyanobacterial concentration after 24 h, and this approximate concentration was then applied to a wastewater treatment pond in the full-scale trial. In the full-scale experiment, intense spatial and temporal monitoring of phytoplankton concentrations and temperature throughout the pond was performed. Cyanobacterial biomass was reduced by 57% and total phytoplankton biomass by 70% within 48 h of H2O2 addition. Mixing and radiation were shown to control the depth reached by H2O2 following addition to the ponds. The synergistic effect of H2O2 addition with environmental factors increased the effectiveness of cyanobacterial removal compared with laboratory experiments. The concentration of H2O2 required for the removal of cyanobacteria under field conditions may be decreased from laboratory studies by an order of magnitude.