Phytoplankton blooms containing elevated levels of cyanobacteria are common in wastewater treatment plants. Microcystis aeruginosa, the most common freshwater cyanobacterial species, produces the hepatotoxin microcystin, which is a threat to human and environmental health. Blooms also affect the viability of treating and reusing water and cause problems when detritus accumulates in pipe and pumping delivery infrastructure. We proposed the application of hydrogen peroxide (H2O2) to induce cyanobacterial cell death. Spectral fingerprinting of phytoplankton into four groups (cyanobacteria, chlorophyta, diatoms, and cryptophyta) allowed for determination of equivalent chlorophyll-a (chl-a) concentrations contributed by photosynthetic pigments, an indicative measure of the photosynthetic activity of each phytoplankton group. This was used to establish the effect of H2O2 addition on phytoplankton in wastewater samples. The lowest H2O2 dose that caused statistically significant exponential decay of phytoplankton groups was approximately 3.0 × 10−3 g H2O2/μg phytoplankton chl-a. At this dose, cyanobacteria and total phytoplankton exhibited a half-life of 2.3 and 4.5 h, respectively. Cyanobacteria decayed at a rate approximately twice that of chlorophyta and diatoms, and the combined chl-a of all phytoplankton groups decreased to negligible levels within 48 h of H2O2 application.