Natural organic matter is an important component in terrestrial surface environment. More and more researches indicatedthat it plays an important role in physical, chemical and biological processes of terrestrial ecosystem;it is the important cycling routesof matter and energy and relates with nearly all the important links of ecosystem. Natural organic matter is not only the importantstudy field of biogeochemistry, ecology and environment sciences, but also a basic theoretical area in the assessment, prediction andcontrol of environment pollution. Natural organic matter now becomes the focus of environment quality, toxicology, environment lawand management. Using fresh lake and river as examples, this article briefly summarizes the study results of sources, chemicalstructure, cycling characteristics, coupling relations with nutrients cycling, and its effects on mobility and transformafion of toxicmetals and organic pollutants, and expounds the possible right research directions and contents referring to water eutrophication andenvironment pollution. This article also makes a prospect about modern organic environment and biogeochemistry.