This study aims at mathematical modeling of systemic factors threatening the sanitary and hygienic state of sources of water supply. It is well-known, that this state affects health of population consuming water from different water sources (lakes, reservoirs, rivers). In particular, water quality problem may cause allergic reactions that are the important problem of health care. In the paper, the authors present the mathematical model, that enables on the basis of observations of a natural system to predict the system's behavior and determine the risks related to deterioration of drinking water resources. As a case study, we uses supply of drinking water from Lake Sevan, but the approach developed in the study can be applied to wide area of adjacent problems.