Oxidative processes play an important role both in assessing the quality of natural waters and in the metabolism regulation in biological objects of varying complexity. Any biologically active substances, when ingested, affect the intensity of lipid peroxidation processes (LPO) and the structural state of biological membranes (Burlakova, 2005). Previously, the similarity functioning of the physico-chemical system of LPO regulation on the membrane and organ levels was revealed (Shishkina et al., 2013). This made it possible to consider the LPO regulation system as the basis for environmental monitoring and to propose a model system of spontaneous lecithin oxidation to assess the effects of toxicants on biological objects (Shishkina et al., 2020, 2021). The purpose of this work was to study the effect of natural waters on the physico-chemical properties of the membranes of biological objects, using the ability of natural phospholipids to form nanosize particles in a polar medium. The objects of the study were samples of the rivers Dubna and Sestra (Moscow region), Usman (Voronezh region), Don (Rostov region) and well water (Voronezh Reserve). The analogue of natural phospholipids was soy bean lecithin, which contains from 55% to 80% phospholipids in total lipids. Using the methods of thin-layer chromatography, dynamic light scattering, UV spectrometry, the following indicators were measured: the hydrochemical composition of water, the size of lecithin micelles, their Z-potential, UV spectra of lecithin solutions and their mathematical processing using the Gauss method. The results obtained are discussed from the point of view of the influence of the hydrochemical composition of natural water on the physico-chemical properties of natural phospholipids and the search of new indicators for assessing the state of natural waters.