Ammonia and greenhouse gases have a negative impact on the environment. The most important agricultural sources of ammonia are dairy cattle housing systems, which are mainly naturally ventilated. Estimating emissions for naturally ventilated barns (NVB) is challenging due to the large number of influencing factors. Most notably, the direct coupling of the inside flow regime with ambient and turbulent weather conditions causes difficulties in measuring ventilation rates, gas concentrations and emissions; thus, different methods are available. In this study, we compared the outputs of total volume flow obtained by two indirect methods (CO2 mass balance) to the direct method. The latter we assume in this study as the reference method since it is a fundamental approach that estimates airflow on the inlet. In the context of mass balancing, we compared wind related (sampling method 1) and non-wind related (sampling method 2) approaches for measuring CO2 concentrations. The total volume flow calculations were based on hourly measurements of CO2 concentrations obtained by Fourier transform infrared (FTIR) spectrometer. Data were collected over a period of six months. The values of the total volume flow were filtered for prevailing southern winds (90∘ angle). The wind related method (sampling method 1) in stable cross-inflow conditions produces more accurate and realistic values in terms of the general representation of the values in comparison with direct method and can be considered further for measurements of volume flow in the NVBs.