The purpose of the research is to consider the peculiarities of different ways of managing natural resources, especially land (land plots), in the context of the sustainable development of territories within the special economic zones of Russia. The authors distinguish the management of natural resources depending on their form of ownership, giving special preference to the private form of ownership, as a direct way of managing natural resources in agricultural cooperation. The international experience of natural resources management has shown the dependence of urbanization and the quality of the state of ecology in specially designated territories and made it possible to identify areas for improving the management of natural resources in Russia. The digital transformation of natural resource management has been identified as a priority in the context of pandemic, but it does not exclude physical participation (control) in resource use. The need to implement a differentiated foreign policy on the management of natural resources in the border territories was identified, since the specificity of the mentality of the peoples integrating in these territories is based on exclusively consumer interest in access to the natural resources of such regions, the desire to use the transit potential of Russia, but not the desire to develop and preserve the border territorial space. In principle, research on natural resource management is carried out from the point of view of public administration, not taking into account the management of land, as the largest resource, by private owners, which has a decisive influence on the sustainable development of the territory. The results take into account the optimal management of natural resources using modern digital technologies and are aimed at the conservation and rational use of resources, especially in border areas located in special economic zones, which is especially important for maintaining the geopolitical integrity of the territory.