We have systematically studied the inability of boundary layer turbulence to efficiently mix reactive species. This creates regions where the species are accumulated in a correlated or anti-correlated way, thereby modifying the mean reactivity. Here, we quantify this modification by the intensity of segregation, <i>I</i><sub>S</sub>, and analyse the driving mechanisms: heterogeneity of the surface moisture and heat fluxes, various background wind patterns and non-uniform isoprene emissions. For typical conditions in the Amazon rain forest, applying homogeneous surface forcings, the isoprene-OH reaction rate is altered by less than 10 %. This is substantially smaller than the previously assumed <i>I</i><sub>S</sub> of 50 % in recent large-scale model analyses of tropical rain forest chemistry. Spatial heterogeneous surface emissions enhance the segregation of species, leading to alterations of the chemical reaction rates of up to 20 %. For these cases, spatial segregation is induced by heterogeneities of the surface properties: a cool and wet forested patch characterized by high isoprene emissions is alternated with a warm and dry patch that represents pasture with relatively low isoprene emissions. The intensities of segregation are enhanced when the background wind direction is parallel to the borders between the patches and reduced in case of a perpendicular wind direction. The effects of segregation on trace gas concentrations vary per species. For the highly reactive OH, the differences in concentration averaged over the boundary layer are less than 2 % compared to homogeneous surface conditions, while the isoprene concentration is increased by as much as 12 % due to the reduced chemical reaction rates. These processes take place at the sub-grid scale of chemistry transport models and therefore need to be parameterized.