The treatment and control of cyanobacterial blooms using copper-based algaecides in water reservoirs have historically been used; however, due to the adverse impact of copper on the environment, water authorities have been researching and studying new and innovative ways to control cyanobacterial blooms. Hydrogen peroxide has been investigated as an environmentally friendly alternative, and this research aims to determine the impact of water quality on its effectiveness based on the decay characteristics in different water samples. Natural water samples from South Australian reservoirs and river were used to evaluate hydrogen peroxide decomposition and provide a better strategy for water operators in using it as an algaecide. Our experiments show the dependency of hydrogen peroxide decomposition not only on water quality but also on the initial hydrogen peroxide dose. A higher initial hydrogen peroxide dose can trigger the increase of pH, leading to increased consumption of hydrogen peroxide. In addition, the hydrogen peroxide decomposition is significantly accelerated with the rise of copper concentration in water samples. Moreover, it is found that UV light can also affect the decomposition rate of hydrogen peroxide. The hydrogen peroxide decay is more significant under UV light for the samples with lower hydrogen peroxide concentrations. Our study also shows the impact of dissolved organic carbon (DOC) on hydrogen peroxide decomposition is not substantial. The study also presents a modelling method to optimise hydrogen peroxide application based on water quality characteristics. Our findings can provide knowledge for the water industry to produce a suitable model which can be used to optimise the application of hydrogen peroxide for the control of cyanobacteria.