A large eddy simulation (LES) model coupled with O-NO-VOC chemistry is implemented to simulate the coupled effects of emissions, mixing and chemical pre-processing within an idealised deep (aspect ratio = 2) urban street canyon under a weak wind condition. Reactive pollutants exhibit significant spatial variations in the presence of two vertically aligned unsteady vortices formed in the canyon. Comparison of the LES results from two chemical schemes (simple NO-O chemistry and a more comprehensive Reduced Chemical Scheme (RCS) chemical mechanism) shows that the concentrations of NO and O inside the street canyon are enhanced by approximately 30-40% via OH/HO chemistry. NO, NO, O, OH and HO are chemically consumed, while NO and O (total oxidant) are chemically produced within the canyon environment. Within-canyon pre-processing increases oxidant fluxes from the canyon to the overlying boundary layer, and this effect is greater for deeper street canyons (as found in many traditional European urban centres) than shallower (lower aspect ratio) streets. There is clear evidence of distinct behaviours for emitted chemical species and entrained chemical species, and positive (or negative) values of intensities of segregations are found between pairs of species with similar (or opposite) behaviour. The simplified two-box model underestimated NO and O levels, but overestimated NO levels for both the lower and upper canyon compared with the more realistic LES-chemistry model. This suggests that the segregation effect due to incomplete mixing reduces the chemical conversion rate of NO to NO. This study reveals the impacts of nonlinear O-NO-VOC photochemical processes in the incomplete mixing environment and provides a better understanding of the pre-processing of emissions within canyons, prior to their release to the urban boundary layer, through the coupling of street canyon dynamics and chemistry.