The author analyzes the legal order of granting lands, land plots and forest plots, water objects, their parts allocated for conducting the works related to subsoil use, as well as legal regulation of the establishment of their boundaries. He considers various approaches to the recognition of such objects as independent objects of the environmental management right, and describes certain requirements to establish the properties and signs promoting their identification. Terminological shortcomings of the Russian ecological legislation and features of the legal regime of land and forest plots, water objects allocated for geological exploration and mineral extraction are mentioned. It is emphasized that such features are defined by the natural characteristics of environment components, by the branch approach to designing the mode of their use, and by the establishment of various forms of ownership and title rights to them. The sequence and interdependence of nature users’ actions for the registration of their subsoil rights are assessed. On the basis of certain examples of court practice, the author examines some problems related to the change and specification of the boundaries of subsoil plots. He puts forth some proposals for the elimination of shortcomings of the legal regulation of the complex use of natural resources.