Naturally occurring Au nanoparticles (AuNPs) have been widely observed in ore deposits, coal, soil, and environmental water. Identifying the source of these naturally occurring AuNPs could be helpful for not only the discovery of Au deposits through advanced exploration methods, but also the elucidation of the biogeochemical cycle and environmental toxicity of ionic Au and engineered AuNPs. Here, we investigated the effect of natural/simulated sunlight and heating on the reduction of ionic Au by ubiquitous dissolved organic matter (DOM) in river water. The reductive process probed by X-ray photoelectron spectroscopy revealed that phenolic, alcoholic, and aldehyde groups in DOM act as reductive sites. Long-time exposure with thermal and photoirradiation induced the further fusion and growth of AuNPs to branched Au nanostructure as precipitation. The formation processes and kinetics of AuNPs were further investigated using humic acid (HA) as the DOM model, with comprehensive characterizing methods. We have observed that HA can reduce ionic Au(III) complex (as chloride or hydroxyl complex) to elemental Au nanoparticles under sunlight or heating. In this process, nearly all of the Au(III) could be reduced to AuNPs, in which HA serves as not only the reductive agent, but also the coating agent to stabilize and disperse AuNPs. The size and stability of AuNPs were highly dependent on the concentration ratio of Au(III) to HA. These results imply that, besides biological processes, this thermal or photochemical reduction process is another possible source of naturally occurring AuNPs in natural environments, which possibly has critical impacts on the transport and transformation of Au and engineered AuNPs.