Abstract. During the Biosphere Effects on AeRosols and Photochemistry EXperiment 2007 (BEARPEX-2007), we observed eddy covariance (EC) fluxes of speciated acyl peroxy nitrates (APNs), including peroxyacetyl nitrate (PAN), peroxypropionyl nitrate (PPN) and peroxymethacryloyl nitrate (MPAN), above a Ponderosa pine forest in the western Sierra Nevada. All APN fluxes are net downward during the day, with a median midday PAN exchange velocity of −0.3 cm s −1 ; nighttime storage-corrected APN EC fluxes are smaller than daytime fluxes but still downward. Analysis with a standard resistance model shows that loss of PAN to the canopy is not controlled by turbulent or molecular diffusion. Stomatal uptake can account for 25 to 50% of the observed downward PAN flux. Vertical gradients in the PAN thermal decomposition (TD) rate explain a similar fraction of the flux, suggesting that a significant portion of the PAN flux into the forest results from chemical processes in the canopy. The remaining "unidentified" portion of the net PAN flux (∼15%) is ascribed to deposition or reactive uptake on nonstomatal surfaces (e.g. leaf cuticles or soil). Shifts in temperature, moisture and ecosystem activity during the summerfall transition alter the relative contribution of stomatal uptake, non-stomatal uptake and thermochemical gradients to the net PAN flux. Daytime PAN and MPAN exchange velocities are a factor of 3 smaller than those of PPN during the first two weeks of the measurement period, consistent with strong intra-canopy chemical production of PAN and MPAN Correspondence to: J. A. Thornton (thornton@atmos.washington.edu) during this period. Depositional loss of APNs can be 3-21% of the gross gas-phase TD loss depending on temperature. As a source of nitrogen to the biosphere, PAN deposition represents approximately 4-19% of that due to dry deposition of nitric acid at this site.