The nocturnal drainage flow of air causes significant uncertainty in ecosystem CO2, H2O, and energy budgets determined with the eddy covariance measurement approach. In this study, we examined the magnitude, nature, and dynamics of the nocturnal drainage flow in a subalpine forest ecosystem with complex terrain. We used an experimental approach involving four towers, each with vertical profiling of wind speed to measure the magnitude of drainage flows and dynamics in their occurrence. We developed an analytical drainage flow model, constrained with measurements of canopy structure and SF6 diffusion, to help us interpret the tower profile results. Model predictions were in good agreement with observed profiles of wind speed, leaf area density, and wind drag coefficient. Using theory, we showed that this one‐dimensional model is reduced to the widely used exponential wind profile model under conditions where vertical leaf area density and drag coefficient are uniformly distributed. We used the model for stability analysis, which predicted the presence of a very stable layer near the height of maximum leaf area density. This stable layer acts as a flow impediment, minimizing vertical dispersion between the subcanopy air space and the atmosphere above the canopy. The prediction is consistent with the results of SF6 diffusion observations that showed minimal vertical dispersion of nighttime, subcanopy drainage flows. The stable within‐canopy air layer coincided with the height of maximum wake‐to‐shear production ratio. We concluded that nighttime drainage flows are restricted to a relatively shallow layer of air beneath the canopy, with little vertical mixing across a relatively long horizontal fetch. Insight into the horizontal and vertical structure of the drainage flow is crucial for understanding the magnitude and dynamics of the mean advective CO2 flux that becomes significant during stable nighttime conditions and are typically missed during measurement of the turbulent CO2 flux. The model and interpretation provided in this study should lead to research strategies for the measurement of these advective fluxes and their inclusion in the overall mass balance for CO2 at this site with complex terrain.