Organic matter is an integral part of the chemical composition of natural waters and plays an important role in collection and migration of chemical elements, including pollutants in water bodies. The article presents the chemical and organic composition of layer waters in the Sovetskoe and Vakhskoe oil deposits in the Tomsk region. Underground waters have chloride and sodium, and a high concentration of organic matter (sorg up to 90 mg/l). The goal of the publication is to identify the main patterns in the distribution of diluted organic matter by groups in layer waters in the south of Western Siberia and determine their potential contribution to the migration and collection of micro-elements. On the basis of the collected data on the group composition of diluted organic matter, it has been established that alkanes, naphthalens, alkyl benzenes, cyclohexanes, phenanthrenes are the most common. The results of the analysis of the micro-element composition of the extracted organic matter from the underground waters show that there is no correlation between the micro-elements composition of the water organic matter and various groups of compounds in it. We have a made suggestion that the key role in the migration and accumulation of micro-elements in water belongs to high-molecular components of organic matter that is characterised by its diverse composition and complex insufficiently studied structure.