The article is devoted to the development of methodical approaches to the management of environmental risks due to pesticide contamination of agrocenoses. An assessment of ecological risks due to the use of pesticides was carried out at the scientific research field of the Skvirskaya research station of organic production of the IAP of the National Academy of Sciences during the growing seasons of 2019–2021. The methods of assessing the ecological risks of potential pesticide contamination of agrocenoses based on the indicators of the agroecotoxicological index (AETI) and the ecotoxic impact of harmful substances (E) were used on the natural environment. It was shown that the level of environmental risk due to the use of pesticides in the research field of the station according to the weighted average indices (AETI) is characterized as low – risk, and the environmental risk due to the pesticides using is minimal. According to indicators of ecotoxicity (E), the pesticides that were used are characterized as having a low potential ecotoxic risk of impact on agrocenoses of cultivated plants. However, the total pesticide ecotoxicological load (ΣЕ = 0.425 compared to the standard EDDT = 1) indicates the possibility of disruption of ecological connectivities in the agroecosystem. One of the elements of environmental risk management can be the assessment of the pesticide load on agroecosystems and considering of the territory ability to self-clean. In order to minimize the environmental risks of pesticide contamination of agrocenoses, measures should be taken to regulate the use of chemical plant protection agents. This can be done by banning or limiting the use of pesticides that have a high level of ecotoxicity and are persistent in the soil. This will contribute to increasing the ecological safety of agro-ecosystems and the natural environment.