The chemical composition of water is determined by the environment with which it comes into contact, with the establishment of a dynamic balance, conditioned by energy and substance flows, expressed by redox equivalents. The valuable biological state of natural waters as a living environment is oxidizing, determined by the presence of hydrogen peroxide. For the characterization of the redox state of the waters, it is not enough to monitor hydrogen peroxide, but it is also necessary to monitor reducing equivalents, such as thiols. The purpose of this chapter is to monitor the content of thiol compounds in some lentic and lotic systems on the territory of the Republic of Moldova for a period of five years. The comparative analysis of the results obtained for rivers and lakes allowed the complex elucidation of the redox state of these waters by characterizing the intensity of redox processes with the participation of thiols. The results indicate that redox processes occur with different intensities in rivers and lakes due to their different chemical composition.