Wastewater stabilization ponds (WSPs) are essential treatment systems for smaller communities, leveraging natural ecological processes for cost-effective and practical wastewater treatment. However, a significant concern regarding WSPs centers on their effectiveness amidst climate change influences. Historical data reveals a 1.7 °C temperature rise across Canada since 1948 with further warming anticipated by the late century (2081–2100) ranging from 1.8 °C to 6.3 °C for low and high-emission scenarios, respectively. These temperature shifts will significantly impact water temperature and thermal profiles within WSPs, altering their thermal stratification and biogeochemical processes. Consequently, these changes will affect the treatment mechanisms necessary for WSP disinfection. This study employs a numerical model for a WSP located in southeastern Ontario, utilizing a Delft-3D FLOW model to replicate pond dynamics. The model underwent calibration using field measurements such as water temperature, flow rate, and stratification data. The calibrated numerical model can simulate predictive scenarios based on projected climatic data. The insights gained from this study aim to enhance understanding of how WSP systems are affected by climate change and how they can be adapted for effective operation to preserve receiving water environments.