Environmental quality management requires the compliance with a number of conditions, such as the use of criteria for the reliable assessment of the health effects of harmful environmental factors (eg., hygienic standards, risk indices) and the optimization of factors of the laboratory control, including chemicals. The A.N. Sysin Research Institute of Human Ecology and Environmental Health (now part of the Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”) of the Ministry of Health of the Russian Federation has corrected domestic hygienic standards of chemicals in the water of water bodies in accordance with international recommendations, and standards of substances in ambient air - according to time characteristics and MPC values. Unified standards in water for substances belonging to the same structural class and not differing in the mechanism of action are justified, hygienic standards for a mixture of substances in atmospheric air have been established according to the criterion “obsession of the smell”. The developing methods of predicting the toxicity of substances make it possible to improve the planning of experiments in selecting doses and indices of the state of the organism. On more than 50 territories of the Russian Federation, a health risk assessment under the influence of chemical environmental factors was implemented. At the same time, an adequate assessment and control of environmental pollution are hindered by a number of circumstances, first of all, the lack of an optimal monitoring system and imperfection of its organization. Studies have shown the number of control indices from a few units to several tens, while hundreds of components that are not provided with regulations are identified. This is due to the lack of modern equipment and analytical methods. The solution to the problem lies in the systematic application of the methodology for selecting priority indices for monitoring. At the same time, an attempt to replace the assessment of the hazard of substances’ harmful effects on the body using generalized indices, for example, a unified “interagency index”, is untenable. The developed recommendations are aimed at improving the organization and methodology of environmental quality management.