Organic matter (OM) in aquatic system is originated from autochthonous and allochthonous natural sources as well as anthropogenic inputs, and can be found in dissolved, particulate or colloidal form. According to the type/composition, OM can be divided in non-humic substances (NHS) or humic substances (HS). The present review focuses on the main groups that constitute the NHS (carbohydrates, proteins, lipids, and lignin) and their role as chemical biomarkers, as well as the main characteristics of HS are presented. HS functions, properties and mechanisms are discussed, in addition to their association to the fate, bioavailability, and toxicity of organic microcontaminants in the aquatic systems. Despite the growing diversity and potential impacts of organic microcontaminants to the aquatic environment, limited information is available about their association with OM. A protective effect is, however, normally seen since the presence of OM (HS mainly) may reduce bioavailability and, consequently, the concentration of organic microcontaminants within the organism. It may also affect the toxicity by either absorbing ultraviolet radiation incidence and, then, reducing the formation of phototoxic compounds, or by increasing the oxygen reactive species and, thus, affecting the decomposition of natural and anthropogenic organic compounds. In addition, the outcome data is hard to compare since each study follows unique experimental protocols. The often use of commercial humic acid (Aldrich) as a generic source of OM in studies can also hinder comparisons since differences in composition makes this type of OM not representative of any aquatic environment. Thus, the current challenge is find out how this clear fragmentation can be overcome.