Large animals such as sika deer are considered to have diverse impacts on the aboveground and belowground processes in terrestrial ecosystems. Previous studies on the ecological impacts of deer grazing have been mostly conducted in open ecosystems where the home ranges of the deer are not restricted; however, few studies have been conducted in closed ecosystems. The present study was carried out to investigate the impact of deer on soils and plants in Nakajima Island in Lake Toya, where sika deer populations are dense within the closed ecosystem. We used six deer fences on the island and examined the physical and chemical properties of soils along with the chemical properties of plants. The thickness of litter layer on the soil surface was smaller and the surface soil hardness was larger outside the fences than inside. In addition, the soil nitrogen characteristics inside and outside the fence varied with the locations, especially the grassland soil outside the fence had higher nitrate-N than the forests. Similarly, nitrogen concentrations in Japanese spurge leaves were significantly higher outside the fences in the grassland than inside. These results suggest that in Nakajima Island, increased density of deer variously changes the physical properties of the soils and the chemical properties of the soils and plants, and these changes vary based on deer abundance and vegetation type. Because ranges for the movement of deer are limited in Nakajima Island, the effects of high deer density could be observed over the island, and stabilized for long time.