Emissions from aviation sources typically represent a small portion of the total emissions in an air quality region. However, given the projected growth in aviation transport and the continued decrease of emissions from most other anthropogenic sources, the analysis of emissions from aviation is of increased importance to understand their impacts on air quality. The Federal Aviation Administration (FAA) Emissions and Dispersion Modeling System (EDMS) is the required model for performing air quality analysis of aviation sources in the United States and is typically used to analyze changes to local air quality in the vicinity of individual airports. In the public release, EDMS computes spatially and temporally allocated emissions for use with the American Meteorological Society/EPA Regulatory Model (AERMOD) for estimating pollutant concentrations. The EPA National Emission Inventory (NEI) is used to support local- and regional-scale air quality modeling. Currently, aircraft emissions are represented as surface-level emissions by county in the NEI. However, given that aviation sources, and their emissions, operate in a three-dimensional environment, air quality models can benefit from emissions data that are more realistically spatially allocated. To provide realistic three dimensional representations of all aviation emissions, we developed an interface to the Sparse Matrix Operator Kernel Emissions (SMOKE) modeling system called EDMS2Inv that accepts the AERMOD-ready spatially and temporally allocated (hourly) emissions inventory from EDMS for direct use in the Community Multiscale Air Quality (CMAQ) model. This paper describes the implementation of this improved representation of aviation emissions from three airports (Atlanta - Hartsfield, Chicago - O'Hare and Providence - T.F. Green) using the new link from EDMS to CMAQ, and the results from annual CMAQ simulations with an emphasis of the contribution of aircraft emissions below 3,000 meters on predicted ozone and PM_2.5.