The Indianapolis Flux Experiment (INFLUX) aims to use a top-down inversion methodology to quantify sources of Greenhouse Gas (GHG) emissions over an urban domain with high spatial and temporal resolution. Analyzing the contribution of different source types or sectors is a fundamental step in order to achieve an accuracy level desired for such applications. To this end, the Weather Research and Forecasting model (WRF-ARW) was used along with a modified version of the GHG chemistry module for simulating the CO2 mole fraction transport during September and October 2013. Sectoral anthropogenic CO2 emissions were obtained from Hestia 2013 and from Vulcan 2002. Biogenic CO2 emissions were simulated by using an augmented version of the “Vegetation Photosynthesis and Respiration Model” (VPRM) included in WRF-CHEM. The atmospheric model performed well in capturing day to day variability of the concentration. The errors were largely reduced during the well-mixed conditions indicating that a large share of the errors was due to the misrepresentation of nighttime stable conditions in the model, causing an overestimation of the nighttime peaks. In general, the averaged daily cycle was well represented by the model. In addition, 4 towers presented a slightly delayed collapse of the nocturnal stable boundary layer. Last, the biogenic contribution was important, being larger than the anthropogenic contribution for 7 out of 12 towers during this period. In general, the anthropogenic contribution was dominated by the Electricity Production, 6.5% to 39%, Mobility, 11% to 56%, and Industrial sectors, 4.8% to 10%.