The priorities of sustainable development, recognized by the global community, are based on the environmental, social, and corporate agendas. The achievement of the Sustainable Development Goals, approved by the General Assembly of the United Nations, implies the involvement of both society and the state in this process. To measure the results of government bodies’ activities in this area, it is necessary to establish directions, indicators, and methodological approaches that allow for assessing their contribution to achieving priority goals. The aim of the study is to substantiate the directions and tools for analyzing the activities of customs authorities in terms of ensuring both the environmental agenda and sustainable development of regions. The scientific methods include the monographic method, methods of time series analysis, tabular and graphical methods. Results: we have identified the areas of influence of customs authorities on the achievement of sustainable development goals and recognized trends in the volume of imports to Russia when applying preferential measures for developing and least developed countries. We assessed the effectiveness of these measures and developed a methodology for determining the impact of the customs activity in the preferential regime on the state budget. The authors also assessed the contribution of customs authorities to the implementation of environmental agendas through the administration of recycling fees.