An autonomous facility for storing spent nuclear fuel includes a building forming an enclosed interior space containing a water-filled spent fuel pool. The pool includes fuel racks containing spent fuel assemblies which heat the water via radioactive decay. A passive cooling system includes a submerged heat exchanger in the pool and an air cooled heat exchanger located in ambient air outside the building at a higher elevation than the pool heat exchanger. A heat transfer working fluid circulates in a closed flow loop between the heat exchangers via unpumped natural gravity driven flow to cool the fuel pool. The air cooled heat exchanger may be enclosed in a concrete reinforced silo adjoining the building for impact protection. The building may include a cask pit formed integrally with the pool to allow fuel assembles to be removed from a transport cask and loaded into the fuel rack underwater.