This study was conducted to find out characteristics of trace element levels and those impacts to organisms at a former uranium (U) mining site. Concentrations of trace elements (Li, Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Mo, Cd, Cs, Ba, Pb, Bi, and U) were determined in sediments, water, and three organism types (insects, frogs, and newts) from three zones in the former U mining site, Ningyo-toge in Japan. Concentrations of As and U in the sediments and water samples were the highest at the mill tailings pond (MP) site, where post-U extraction remnants have been accumulated. Additionally, among the organisms analyzed the highest concentrations of these elements/isotopes were found in newts from MP. Considering data analyses of the whole-body element concentrations, bioaccumulation factors, and δ15N values for the organisms, it was concluded that newts might be the most vulnerable species in this location. Further monitoring and more accurate evaluation of the ecological impacts are preferred for this former U mining site.