Global and regional chemical transport models of the atmosphere are based on the assumption that chemical species are completely mixed within each model grid box. However, in reality, these species are often segregated due to localized sources and the influence of topography. In order to investigate the degree to which the rates of chemical reactions between two reactive species are reduced due to the possible segregation of species within the convective boundary layer, we perform large-eddy simulations (LESs) in the mountainous region of Hong Kong Island. We adopt a simple chemical scheme with 15 primary and secondary chemical species, including ozone and its precursors. We calculate the segregation intensity due to inhomogeneity in the surface emissions of primary pollutants and due to turbulent motions related to topography. We show that the inhomogeneity in the emissions increases the segregation intensity by a factor of 2–5 relative to a case in which the emissions are assumed to be uniformly distributed. Topography has an important effect on the segregation locally, but this influence is relatively limited when considering the spatial domain as a whole. In the particular setting of our model, segregation reduces the ozone formation by 8 %–12 % compared to the case with complete mixing, implying that the coarse-resolution models may overestimate the surface ozone when ignoring the segregation effect.