Abstract. We use H₂O_v isotopic vertical profile measurements and complementary meteorological observations to examine how boundary layer, cloud, and mixing processes influence the vertical structure of deuterium-excess (d-excess = δD – 8 × δ¹⁸O) in the boundary layer, inversion layer, and lower free troposphere. Airborne measurements of water vapor (H₂O_v) stable isotopologues were conducted around two continental U.S. cities in February–March 2016. Nine research flights were designed to characterize the δD, δ¹⁸O, and d-excess vertical profiles extending from the surface to ≤ 2 km. We examine observations from three unique case study flights in detail. One case study shows H₂O_v isotopologue vertical profiles that are consistent with Rayleigh isotopic distillation theory coinciding with clear skies, dry adiabatic lapse rates within the boundary layer, and relatively constant vertical profiles of wind speed and wind direction. The two remaining case studies show that H₂O_v isotopic signatures above the boundary layer are sensitive to cloud processes and complex air mass mixing patterns. These two case studies indicate anomalies in the d-excess signature relative to Rayleigh theory, such as low d-excess values at the interface of the inversion layer and the free troposphere, which is possibly indicative of cloud evaporation. We discuss possible explanations for the observed d-excess anomalies, such as cloud evaporation, wind shear, and vertical mixing. In situ H₂O_v stable isotope measurements, and d-excess in particular, could be useful for improving our understanding of moisture processing and transport mixing occurring between the boundary layer, inversion layer, and free troposphere.