Old-growth forests play essential roles in maintaining biodiversity and providing ecosystem services. While heterogeneity produced by various natural disturbances and micro-topography is an integral part of old-growth forest ecosystems, the effects of such natural disturbances and heterogeneity on arthropod diversity in old-growth forests are not fully understood. In this study, we evaluated how the heterogeneity produced by treefalls, landslides, and streams influences ground beetle diversity in an old-growth beech forest in the Tadami Biosphere Reserve, Japan. Fourteen plots composed of five forest interior, three treefall gaps, three landslides, and three along a stream were established, with 15 pitfall traps installed in each plot. Traps were opened for two days in each season. The results showed that canopy openness was the highest in landslide gaps, whereas litter depth was the lowest along the stream. Species richness was lowest along the stream but was similarly high in the other three habitat types. The activity density of beetles was also lowest along the stream, but highest in the landslide gaps. Landslide gaps and streams had distinct species compositions and several indicator species, respectively, indicating that soil disturbances involved in landslides and repeated overflow by snowmelt and heavy rain along the stream provide specific environmental conditions that differ from the forest interior and treefall gaps. This study demonstrates that heterogeneity derived from natural disturbances and streams enhances biodiversity in old-growth forests. These findings can be used to develop management measures that mimic natural disturbances in order to conserve biodiversity in managed forests.