The advancement of nanotechnology has made more attention on synthetic nanoscale particles, while naturally nanoscale particles are often overlooked, especially nearly or nanoscale natural amorphous particles (nearly or NNAPs). Here, we report nearly or NNAPs obtained from multiple media for discussing their geochemistry environmental implications in eight deposits with different minerals and background areas. Internal nanoscale arrangement, elemental composition, and structure of nearly or NNAPs were characterized via high-resolution transmission electron microscopy. The results show nearly or NNAPs are widespread compounds and have a large number. We established the elemental combination relationship and defined them as a native metal, S–O-, P–O-, and Cl–(O)-bearing as well as oxide nearly or NNAPs. Nearly or NNAPs could as a substance migration form by themselves and using as carriers. With strong geochemical features, nearly or NNAPs can carry high proportion of ore-related metal elements from the concealed ore bodies to the surface, indicating the environmental risks of nearly or NNAPs.