In the present study is carried out a comprehensive analysis of the calculation methodology of emissions charges for stationary sources, of damages caused on the atmospheric air and its applying in the Northern Region of the Republic of Moldova. Also, was evaluated the provisions of the Contravention Code regarding the sanctioning for the violation of the atmospheric air protection legislation and actual mechanism of application of fines and of damage compensation in this field in region of study. Were identified the main gaps in the methodology for calculating emissions charges and of damages caused to the atmospheric air, the key problems in the application of the economic instruments for regulating the anthropogenic impact on the atmospheric air, are proposed recommendations for improving the assessment methodology and the procedure for their application.