There are many volcanoes and hot springs in Japan; therefore, many geological layers inherently contain substantial amounts of heavy metals originating from hydrothermal alternation processes. The toxicities of heavy metals contained in geological layers have long been recognized as health and/or environmental risks from the development of metal or non-metal resources in mining areas. Recently, the environmental impacts of naturally-originating heavy metals during construction work for civil engineering purposes, such as roads and tunnels, have been recognized to raise similar risks.The Soil Contamination Countermeasures Law enforced in 2003 defines responsible corporations in charge of preventing environmental contamination of the ground, and stipulates technical aspects regarding investigation surveys and countermeasure techniques. This law mainly covers soil contamination cases, especially in urban areas, to preserve human health. Therefore, it has not been able to deal fully with the environmental impacts of contamination by toxic heavy metals due to construction work not only in urban areas but also in suburban areas.The intent of this paper is to review and discuss chemical characteristics and environmental impacts of naturally-occurring heavy metals. Furthermore, some case studies on necessary assessment methodologies and countermeasures techniques are introduced.