The potential environmental risks of engineered nanoparticles in aquatic environment have attracted considerable attention, but naturally produced nanoparticles have relatively been ignored, such as ore-related nanoparticles. To obtain more information about the natural ore-related nanoparticles, deep groundwater and well water samples were respectively collected in or around four major metal deposits in Inner Mongolia, China. These water samples were tested with high resolution transmission electron microscopy (TEM) and abundant metal-containing nanoparticles were found. Major ore-forming elements of corresponding metal deposits, such as Fe, Pb, Zn and Cu, and even associated elements, such as As, Sb, Sn and Cr, significantly contributed to the chemical compositions of these detected nanoparticles. Through comparison analyses, these metal-containing nanoparticles were shown to be originally from deep concealed metal deposits. They were the products of faulting and oxidation of ore minerals, and were transported long distances by water flow. Notably, these ore-related nanoparticles happened to have similar components with those nanoparticles of high environmental risks. Coupled with the analytical results of Atomic absorption spectroscopy (AAS) and inductively coupled plasma mass spectrometry (ICP-MS), it is recommended that the concentration limits of metal-containing nanoparticles should be considered in the safety assessment of drinking water. This is the first time, so far as we know, that naturally produced ore-related nanoparticles in the aquatic environment were listed as a kind of material with environmental risks. Considering the wide distribution of concealed metal deposits, more attention on related studies was urgently required for establishing specialized risk assessment and monitoring system.