The State Water Register constitutes a fundamental mechanism for systematizing information on water bodies located within the territory of the Russian Federation. Its database aggregates data on water bodies, the nature of their exploitation, the boundaries of water protection zones, as well as other characteristics that are material to the legal regulation of water use. At present, the territorial subdivisions of the Federal Agency for Water Resources refuse to register in the SWR permitting documentation concerning water bodies in the absence of information reflecting the extent to which the body has been studied. The implementation of this mechanism entails the emergence of numerous legal conflicts relating to the registration of insufficiently studied or entirely unstudied water bodies. This article attempts to systematize the principal legal contradictions accompanying the process of including such bodies in the register, to identify existing legislative gaps, and to formulate potential approaches to overcoming them.