Air temperature Ta, specific humidity q, CO2 mole fraction χc, and three-dimensional winds were measured in mountainous terrain from five tall towers within a 1 km region encompassing a wide range of canopy densities. The measurements were sorted by a bulk Richardson number Rib. For stable conditions, we found vertical scalar differences developed over a “transition” region between 0.05 < Rib < 0.5. For strongly stable conditions (Rib > 1), the vertical scalar differences reached a maximum and remained fairly constant with increasing stability. The relationships q and χc have with Rib are explained by considering their sources and sinks. For winds, the strong momentum absorption in the upper canopy allows the canopy sublayer to be influenced by pressure gradient forces and terrain effects that lead to complex subcanopy flow patterns. At the dense-canopy sites, soil respiration coupled with wind-sheltering resulted in CO2 near the ground being 5–7 μmol mol−1 larger than aloft, even with strong above-canopy winds (near-neutral conditions). We found Rib-binning to be a useful tool for evaluating vertical scalar mixing; however, additional information (e.g., pressure gradients, detailed vegetation/topography, etc.) is needed to fully explain the subcanopy wind patterns. Implications of our results for CO2 advection over heterogenous, complex terrain are discussed.