The significance of air flow within dense canopies situated on hilly terrain is not in dispute given its relevance to a plethora of applications in meteorology, wind energy, air pollution, atmospheric chemistry and ecology. While the mathematical description of such flows is complex, progress has proceeded through an interplay between experiments, mathematical modelling, and more recently large‐eddy simulations (LESs). In this contribution, LES is used to investigate the topography‐induced changes in the flow field and how these changes propagate to scalar transport within the canopy. The LES runs are conducted for a neutral atmospheric boundary layer above a tall dense forested canopy situated on a train of two‐dimensional sinusoidal hills. The foliage distribution is specified using leaf area density measurements collected in an Amazon rain forest. A series of LES runs with increasing hill amplitude are conducted to disturb the flow from its flat‐terrain state. The LES runs successfully reproduce the recirculation region and the flow separation on the lee‐side of the hill within the canopy region in agreement with prior laboratory and LES studies. Simulation results show that air parcels released inside the canopy have two preferential pathways to escape the canopy region: a “local” pathway similar to that encountered in flat terrain and an “advective” pathway near the flow‐separation region. Further analysis shows that the preferential escape location over the flow‐separation region leads to a “chimney”‐like effect that becomes amplified for air parcel releases near the forest floor. The work here demonstrates that shear‐layer turbulence is the main mechanism exporting air parcels out the canopy for both pathways. However, compared to flat terrain, the mean updraught at the flow separation induced by topography significantly shortens the in‐canopy residence time for air parcels released in the lower canopy, thus enhancing the export fraction of reactive gases.