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A membrane separation of solutions, along with other purification methods, plays an important role in the effective and ecological safety of food production enterprises and is used for softening and demineralization of water, separation, concentration and purification of technological solutions, as well as for other processes. An important problem of membrane and electromembrane separation methods is to increase the used membrane selectivity. Therefore, the aim of this work was to study the structure transformation effect of ion-exchange membranes on a separation processes efficiency of technological solutions and an ecological safety of food production enterprises using the methods of X-ray diffraction analysis and differential scanning calorimetry (DSC). The analysis of the calculated values of crystallinity degree (CD) by X-ray diffractograms allowed us to identify the different effect of water saturation on the studied membranes. The structure of their material changes, which in turn affects the transport characteristics of the membranes, the efficiency of separation and, ultimately, the environmental ecological safety food enterprises. The cation-exchange membrane MK-40L was characterized by an increase in CD by 5.83%, and the anion exchange membrane MA-41P on the contrary was characterized by a decrease in CD by 5.87%. The crystallite sizes were distributed in the range of 0.096-0.345 nm for the MA-41P membrane and 0.096-0.193 nm for the MK-40L membrane. During thermal studies by DSC one endothermic and exothermic sections were revealed on the obtained curves in the temperature range of 30-202 and 202-498 °C for the MK-40L membrane and 30-223 °C and 223-498 °C for the MA-41P membrane, respectively. The endothermic sections of the curves were characterized by one endothermic peak. Four or five pronounced exothermic peaks were registered on the exothermic sections. At the same time, the MK-40L membrane was characterized by more intense peaks in a water-saturated sample and the MA-41P membrane in the dry one.