In both water and air, the interactions of flow, form, and sediment transport vary over several spatial and temporal scales and act as important controls on dune form, spacing, and alignment. In particular, secondary lee-side flow patterns (e.g. separation and reversal cells) have been identified as important controls on transport mechanics and dune maintenance. However, due to lee-side flow complexity, conventional boundary layer approaches do not adequately account for windspeed response, wind flow patterns, and resultant sediment transport. The purpose of this study is to investigate the role of secondary lee-side flow patterns in the morphodynamics of transverse aeolian dunes. The research approach consists of two main methodological components: a field study of lee-side windspeed and sediment transport, and a scaled wind tunnel flow simulation. The field study characterizes lee-side airflow and sediment transport patterns using a dense array of anemometers and flux traps in the Silver Peak dunefield, Nevada. The tunnel simulation provides high-resolution measurements of flow turbulence using hot-film anemometers and surface shear stress using Irwin sensors. The results from both components, combined with flow visualization, provide the basis for a conceptual model of lee-side flow that expands on existing models by detailing flow structure, surface shear, and sediment transport over isolated and closely spaced dunes for various incident flow conditions. Results show that boundary layer flow on the stoss is affected by incident flow direction (via changes in effective aspect ratio and fetch distance), sediment transport (via momentum extraction effects), and by dune form and spacing (via pressure effects on the flow field and secondary flow patterns). In the lee, turbulence statistics show a turbulent mixing layer bounding the separation cell. A turbulent shear zone is identified and is thought to control the location of flow re-attachment. The extent and location of this zone is controlled by dune size and spacing. Beyond reattachment, a significant distance (25-30h) is required for boundary layer equilibrium, but development is impeded significantly over closely spaced dunes. Differential flow deflection with height in the lee contributes to the development of secondary flows that drive sediment transport and dune migration in a direction that is oblique to the crestline.