The CMAQ modeling system accounts for chemistry in three phases: gas phase, aerosols (solid or liquid), and aqueous phase. The CMAQ modeling system's existing modules for gas phase chemistry are the Carbon Bond -IV (CB-IV), Regional Acid Deposition Model-2 (RADM2), and Statewide Air Pollution Research Center-99 (SAPRC-99) gas phase mechanisms. Several variations of the base gas-phase mechanisms, with and without aqueous and aerosol chemistry are distributed with CMAQ. With the CMAQ's modularity, it is also possible to create or modify the chemical mechanism.

Gas-phase chemical mechanisms are defined in CMAQ as a series of Fortran include files. Located in subdirectories of the $M3MODEL/include/release directory, corresponding to the mechanism name, these include files define the species, source, reaction parameters, and atmospheric processes (e.g. diffusion, deposition, advection) of the different mechanism species. CMAQ mechanism configuration is more similar to the science module configuration than to the horizontal grid or vertical layer configuration in that the mechanism is defined a compilation and results in executables that are hard-wired to a specific gas-phase mechanism. If you want to change chemical mechanisms between simulations, you must recompile a new executable that includes the desired mechanism configuration.