The increasing demand for sustainable biomass has made microalgae farming into the spotlight as a viable source of biofuels, nutraceuticals, and other valuable products. Raceway ponds are one of the most common systems in algaculture due to their simplicity and cost-effectiveness. However, their efficiency is significantly influenced by surrounding microclimate conditions. In this study, we present a Computational Fluid Dynamics (CFD) analysis aimed at optimizing greenhouse design to enhance microalgae production in a raceway pond housed within a controlled greenhouse environment. The research focuses on evaluating the influence of greenhouse microcli- mate parameters on water’s thermal dynamics in the pond. Simulations were conducted to assess how different greenhouse geometries and ventilation configurations affect the heat exchange between the water surface and air within the greenhouse, as well as the internal flow dynamics, both of which are critical for optimal algae growth. The results provide insights into the optimal greenhouse design parameters that maintain the optimal water temperatures in the pond while minimizing thermal fluctuations to enhance microalgae productivity. Specif- ically, a significant 5 ◦C temperature difference was observed between the pond’s surface and bottom, mainly due to convective heat transfer. Key design factors, such as greenhouse height and ventilation rates, were shown to have a substantial impact on water temperature. The insights gained are essential for optimizing greenhouse design and ventilation strategies to maximize algae growth and production efficiency. This preliminary modeling lays the foundation for future sensitivity analyses aimed at refining the system, ultimately improving algae cultivation in controlled environment agri- cultural systems.