© 2020, Society of Agricultural Meteorology of Japan. All rights reserved. Trace atmospheric gases in the biosphere, such as ozone (O3), nitrogen oxides (NOx), and biogenic volatile organic compounds (BVOCs), can affect the carbon cycle as well as the climate. Vertical profiles of nitric oxide (NO), O3, and volatile organic compound (VOC) concentrations were measured at a Japanese larch (Larix kaempferi) forest in the foothills of Mt. Fuji in Japan over an 11-day period in July 2012. The concentrations of NO and O3 during the day were highest above the canopy and decreased with proximity to the forest floor, but those of the VOCs had minimum and maximum points at different levels within the canopy depending on the species. Inverse multilayer models were applied to identify vertical sink and source distribution of these gases within the canopy. The model estimated that there was higher O3 deposition and absorption at the forest floor than in the canopy layer; therefore, the understory was an important O3 sink within the forest. A strong NO sink was simulated in the trunk space, where loss by reaction with O3 is expected. The sinks and sources of BVOC as well as their oxidized products are simulated in the canopy layer and the forest floor. The sink and source distribution suggested that VOC transportation from the neighboring forest also affected the vertical sink and source distribution within the canopy.