Isolators are commonly used in filling operations of pharmaceutical products. To ensure an aseptic inner environment, isolators are regularly sterilized with vaporized hydrogen peroxide. However, despite extensive purging with air, some residual H2O2 remains within the isolator atmosphere and may thus end up in the liquid pharmaceutical drug product, which subsequently may cause oxidation and impact the product’s safety and efficacy. We aimed to evaluate the extent of this phenomenon and to model it. For that purpose, we studied the diffusion of H2O2 into water contained in small recipients exposed to the atmosphere of a H2O2-sterilized small-scale test isolator. Based on the results, a mechanistic model was proposed to estimate the quantity of H2O2 in the product, taking into account the time, filling volume, H2O2 concentration, and a configuration factor. Afterward, this model was challenged by filling water at a manufacturing scale, and we observed that the diffusion model could predict the trend of increasing H2O2 concentration. However, a consistent difference in H2O2 concentration between the model and the experimental results was observed, suggesting the contribution of another parameter. Our results can be used to predict more accurately H2O2 concentration in a pharmaceutical product at the manufacturing level.