Natural disturbances create spatial patterns of the ecosystem processes and functions in natural forests. However, how dynamics and the spatial structure of forests relate to soil nitrogen dynamics is not well understood. We examined the spatial relationship between the distributions of canopy and understory species, and soil nitrogen dynamics in a natural coniferous-broadleaved mixed forest with a dense understory of Sasa dwarf bamboo in northern Japan. The O horizon was thick where coniferous litter predominated, and it was thin where broadleaved litter predominated. The soil water content was low in areas with a thick O horizon and a high abundance of coniferous trees. The soil nitrate content was low where the soil water content was low, and the soil nitrate content increased linearly with increasing net nitrification potential. These results suggest that the soil nitrate content under the coniferous canopy was lower because of the low nitrification potential of soil microbes in soils with low water contents. The soil nitrate content and nitrification potential were higher in the canopy gap than under the canopy. Our results suggest that forest structure, specifically the thickness of the forest floor, significantly affects the spatial pattern of the soil water content, thereby creating a spatial pattern of soil nitrogen availability at a relatively small scale with flat topography. The higher nitrification potential under the canopy gap could pose a long-term risk of nitrate leaching because of the suppression of the natural regeneration of canopy species by dense Sasa dwarf bamboo in this forest ecosystem.