Chemiluminescence (CL) of acridinium esters (AE) has found widespread use in analytical chemistry. Using the mechanism of the reaction of H2O2 with 10-methyl-9-(p-formylphenyl)acridinium carboxylate trifluoromethanesulfonate and a modified flow injection system, the reaction rates of each step in the mechanism were evaluated and used in a kinetic model to optimize the analysis of H2O2. Operational parameters for a flow injection analysis system (reagent pH, flow rate, sample volume, PMT settings) were optimized using the kinetic model. The system is most sensitive to reaction pH due to competition between AE hydrolysis and CL. The optimized system was used to determine H2O2 concentrations in natural waters, including rain, freshwater, and seawater. The lower limit of detection varied in natural waters, from 352 pM in open ocean seawater (mean, 779 pM +/- 15.0%, RSD) to 58.1 nM in rain (mean, 6,340 nM +/- 0.92%, RSD). The analysis is specific for H2O2 and is therefore of potential interest for atmospheric chemistry applications where organoperoxides have been reported in the presence of H2O2.