This study investigates the air pollutant interactions and emission source contributions to ozone (O3) formation within a complex terrain. Air quality simulations using the Community Multiscale Air Quality (CMAQ) Model focused on vertical distributions of O3 for the July 14–18, 2005 episode in the South Coast Air Basin (SoCAB). The Zero-Out method was applied in sensitivity tests for seven emission source categories. Elevated O3 concentrations were found near the top of the planetary boundary layer (PBL, ~1200 m) and in the free troposphere (~3500 m) over the eastern SoCAB. Low O3 concentrations were found near the surface at the center of the basin due to nitrogen oxide (NO) titration by fresh vehicle exhaust. Sea and land breezes, enhanced by up-slope flows (the “mountain chimney effect”) transported O3 upward. Formation of O3 is sensitive to the H2O2/HNO3 ratio, depending on fresh vs. aged pollutant mixtures. Biogenic emissions were important contributors to O3 formation, both in the SoCAB and at the top of the PBL. In contrast, the highest vehicle contributions to O3 were found far from urban areas and in the lower free troposphere. Vertical cross-sectional analysis provided some insights into the O3 formation and mixing processes present in the SoCAB.