Understanding and predicting complex biological systems are best accomplished through the synthesis and integration of information across relevant spatial, temporal and thematic scales. We propose that mechanistic transport models, which integrate atmospheric turbulence with information on relevant biological attributes, can effectively incorporate key elements of aerial transport processes at scales ranging from a few centimetres and fractions of seconds, to hundreds of kilometres and decades. This capability of mechanistic models is critically important for modelling the flow of organisms through the atmosphere because diverse aerial transport processes — such as pathogen spread, seed dispersal, spider ballooning and bird migration — are sensitive to the details of small-scale short-term turbulent deviations from the mean airflow. At the same time, all these processes are strongly influenced by the typical larger-scale variation in landscape structure, through its effects on wind flow patterns. We therefore highlight the useful coupling of detailed atmospheric models such as large eddy simulations (LES), which can provide a high-resolution description of turbulent airflow, with regional atmospheric models, which can capture the effects of landscape heterogeneity at various scales. Further progress in computational fluid dynamics (CFD) will enable rigorous exploration of transport processes in heterogeneous landscapes.