This study develops a numerical model to evaluate the effectiveness of natural ventilation (NV) by analyzing the concentration difference between indoor and outdoor air and the mean age of air (AoA). A standalone building's indoor and outdoor environments were simulated in a CFD framework to examine interactions between typical atmospheric concentrations and the upper IAQ limits of 400 ppm and 1000 ppm. Both single-side and cross flow ventilation scenarios were modeled, considering windward, tangential, and leeward orientations at stagnant, 0.1, 0.5, and 1.0 m/s air velocities. CO2 concentrations were monitored for 20 min. The study utilized the "SST k-ω model", a coupled algorithm with second-order accuracy. The "species transport" model was used to solve the unsteady flow field and diffusion of multi-component flows. In single-side flow scenarios, it was observed that the decay process accelerated with increasing air velocity as expected. At the end of 20 min, the CO2 concentration decreased between 11% and 42% from 0.1 to 1.0 m/s. Cross flow scenarios showed faster decay, even reaching equilibrium at 0.5 and 1.0 m/s in windward/leeward orientations. In single-side flow models, stagnant air resulted in 2–7% lower CO2 concentrations after 20 min compared to other single-side flow scenarios investigating 0.1 m/s air velocity. Mean AoA was not a reliable indicator for IAQ in scenarios that are investigated in this study; thus, investigating CO2 concentrations in a CFD environment allows a more realistic approach to assess natural ventilation in improving IAQ, creating a useful tool for energy-efficient and healthy building design.