Well planned natural ventilation strategies and systems in the built environments may provide healthy and comfortable indoor conditions, while contributing to a significant reduction in the energy consumed by buildings. Computational Fluid Dynamics (CFD) is particularly suited for modelling indoor conditions in naturally ventilated spaces, which are difficult to predict using other types of building simulation tools. Hence, accurate and reliable CFD models of naturally ventilated indoor spaces are necessary to support the effective design and operation of indoor environments in buildings. This paper presents a formal calibration methodology for the development of CFD models of naturally ventilated indoor environments. The methodology explains how to qualitatively and quantitatively verify and validate CFD models, including parametric analysis utilising the response surface technique to support a robust calibration process. The proposed methodology is demonstrated on a naturally ventilated study zone in the library building at the National University of Ireland in Galway. The calibration process is supported by the on-site measurements performed in a normally operating building. The measurement of outdoor weather data provided boundary conditions for the CFD model, while a network of wireless sensors supplied air speeds and air temperatures inside the room for the model calibration. The concepts and techniques developed here will enhance the process of achieving reliable CFD models that represent indoor spaces and provide new and valuable information for estimating the effect of the boundary conditions on the CFD model results in indoor environments.