The synthesis, stability, and toxicity of engineered metal nanoparticles (ENPs) have been extensively studied during the past two decades. In contrast, research on the formation, fate, and ecological effects of naturally-occurring nanoparticles (NNPs) has become a focus of attention only recently. The natural existence of metal nanoparticles and their oxides/sulfides in waters, wastewaters, ore deposits, mining regions, and hydrothermal vents, as exemplified by the formation of nanoparticles containing silver and gold (AgNPs and AuNPs), Fe, Mn, pyrite (FeS2), Ag2S, CuS, CdS, and ZnS, is dictated largely by environmental conditions (temperature, pH, oxic/anoxic, light, and concentration and characteristics of natural organic matter (NOM)). Examples include the formation of nanoparticles containing pyrite, Cu and Zn-containing pyrite, and iron in hydrothermal vent black smoker emissions. Metal sulfide nanoparticles can be formed directly from their precursor ions or indirectly by sulfide ion-assisted transformation of the corresponding metal oxides under anaerobic conditions. This tutorial focuses on the formation mechanisms, fate, and toxicity of natural metal nanoparticles. Natural waters containing Ag(I) and Au(III) ions in the presence of NOM generate AgNPs and AuNPs under thermal, non-thermal, and photochemical conditions. These processes are significantly accelerated by existing redox species of iron (Fe(II)/Fe(III)). NOM, metal-NOM complexes, and reactive oxygen species (ROS) such as O2˙(-), ˙OH, and H2O2 are largely responsible for the natural occurrence of nanoparticles. AgNPs and AuNPs emanating from Ag(I)/Au(III)-NOM reactions are stable for several months, thus indicating their potential to be transported over long distances from their point of origin. However, endogenous cations present in natural waters can destabilize the nanoparticles, with divalent cations (e.g., Ca(2+), Mg(2+)) being more influential than their monovalent equivalents (e.g., Na(+), K(+)). The toxicity of NNPs may differ from that of ENPs because of differences in the coatings on the nanoparticle surfaces. An example of this phenomenon is presented and is briefly discussed.