Satellite and aircraft observations made during the 2006 Texas Air Quality Study (TexAQS) detected strong urban, industrial and power plant plumes in Texas. We simulated these plumes using the Weather Research and Forecasting-Chemistry (WRF-Chem) model with input from the US EPA's 2005 National Emission Inventory (NEI-2005), in order to evaluate emissions of nitrogen oxides (NO_x = NO + NO₂) and volatile organic compounds (VOCs) in the cities of Houston and Dallas-Fort Worth. We compared the model results with satellite retrievals of tropospheric nitrogen dioxide (NO₂) columns and airborne in-situ observations of several trace gases including NO_x and a number of VOCs. The model and satellite NO₂ columns agree well for regions with large power plants and for urban areas that are dominated by mobile sources, such as Dallas. However, in Houston, where significant mobile, industrial, and in-port marine vessel sources contribute to NO_x emissions, the model NO₂ columns are approximately 50%–70% higher than the satellite columns. Similar conclusions are drawn from comparisons of the model results with the TexAQS 2006 aircraft observations in Dallas and Houston. For Dallas plumes, the model-simulated NO₂ showed good agreement with the aircraft observations. In contrast, the model-simulated NO₂ is ~60% higher than the aircraft observations in the Houston plumes. Further analysis indicates that the NEI-2005 NO_x emissions over the Houston Ship Channel area are overestimated while the urban Houston NO_x emissions are reasonably represented. The comparisons of model and aircraft observations confirm that highly reactive VOC emissions originating from industrial sources in Houston are underestimated in NEI-2005. The update of VOC emissions based on Solar Occultation Flux measurements during the field campaign leads to improved model simulations of ethylene, propylene, and formaldehyde. Reducing NO_x emissions in the Houston Ship Channel and increasing highly reactive VOC emissions from the point sources in Houston improve the model's capability of simulating ozone (O₃) plumes observed by the NOAA WP-3D aircraft, although the deficiencies in the model O₃ simulations indicate that many challenges remain for a full understanding of the O₃ formation mechanisms in Houston.