The article identifies possible challenges and threats to balanced subsoil use, in particular mining, and assesses the danger of effects, which allows to highlight the main ones for elimination. The concept of balanced nature management has been clarified, and evolutionary changes in its content have been found out: from the balance within only the economic subsystem to the balance of all three components: environmental, social and economic. The definition of balanced mining has been formulated. The conceptual and categorical apparatus has been clarified regarding the occurrence of danger to the balanced mining: the definitions of global challenges, internal and external threats and risks, and their relationship to each other. We identify economic, environmental, social and institutional threats, and their structuring in relation to challenges. The methodological foundations of their assessment are developed, which include the fundamental principles of assessment procedures and the methodical tools—guidelines for assessing threats. The assessment procedures involve the calculation of particular indicators for each of the areas of threats; the calculation of general indicators taking into account the weight of particular indicators; and the definition of an integral indicator taking into account the weight of general ones. The classification of the integral indicator has been done with the allocation of four groups of the threats’ danger degrees. The guidelines were tested on the Sverdlovsk region, Russia.