Abstract. In a companion paper, we introduced the Chemistry of Atmosphere-Forest Exchange (CAFE) model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. Here, we apply CAFE to noontime observations from the 2007 Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX-2007). In this work we evaluate the CAFE modeling approach, demonstrate the significance of in-canopy chemistry for forest-atmosphere exchange and identify key shortcomings in the current understanding of intra-canopy processes. CAFE generally reproduces BEARPEX-2007 observations but requires an enhanced radical recycling mechanism to overcome a factor of 6 underestimate of hydroxyl (OH) concentrations observed during a warm (~29 °C) period. Modeled fluxes of acyl peroxy nitrates (APN) are quite sensitive to gradients in chemical production and loss, demonstrating that chemistry may perturb forest-atmosphere exchange even when the chemical timescale is long relative to the canopy mixing timescale. The model underestimates peroxy acetyl nitrate (PAN) fluxes by 50% and the exchange velocity by nearly a factor of three under warmer conditions, suggesting that near-surface APN sinks are underestimated relative to the sources. Nitric acid typically dominates gross dry N deposition at this site, though other reactive nitrogen (NOy) species can comprise up to 28% of the N deposition budget under cooler conditions. Upward NO2 fluxes cause the net above-canopy NOy flux to be ~30% lower than the gross depositional flux. CAFE under-predicts ozone fluxes and exchange velocities by ~20%. Large uncertainty in the parameterization of cuticular and ground deposition precludes conclusive attribution of non-stomatal fluxes to chemistry or surface uptake. Model-measurement comparisons of vertical concentration gradients for several emitted species suggests that the lower canopy airspace may be only weakly coupled with the upper canopy. Future efforts to model forest-atmosphere exchange will require a more mechanistic understanding of non-stomatal deposition and a more thorough characterization of in-canopy mixing processes.