Cities and urban agglomerations have an active anthropogenic impact on all components of the environment, including the hydrosphere as a particularly vulnerable component of the environment. The city of Tomsk is an old industrial city, there are no isolated industrial, residential and green zones, so the pollution of natural waters on its territory is complex. The purpose of this work is to study the ecological state of natural waters of Tomsk, to identify the features of pollution and their possible sources. For this purpose, water samples were taken from various sources, as well as from the Tom and Ushayka rivers.