The presence of large areas of anthropogenic transformation of plant communities with a potentially negative impact on adjacent territories makes it relevant to develop various methods for automated monitoring and modeling of processes occurring in these ecosystems. Based on the results of previous studies of phytocoenoses, the authors selected four groups of indicators for constructing a scenario model: integral characteristics of intrusive plant communities (IPC), including those obtained by using remote dynamic methods; integral indicators of the negative impact of IPC on the adjacent agro-ecosystem; indicators of the distribution of mobile forms of trace elements in the soil; and indicators of soil microbiota. As the result, a hypothetical formula is obtained that allows, with minimal impact on the biosystem of technogenic IPC, to sufficiently reduce its adverse impact on the adjacent agro-ecosystem. Further refinement and dissemination of the scenario model and its connection to databases on plant communities will automatically change the values of the coefficients in the solving equations, thereby providing the most accurate and reliable forecast of the response of agro-ecosystems to various control actions.