The naturalized conservation aquaculture unit (refugium) at Los Lunas Silvery Minnow Refugium is the first purpose‐built, large‐scale conservation aquaculture mesocosm. The refugium is 0.2 ha in area, with 0.11 ha of interconnected water habitats, including a stream with sand bars, five ponds, shelves, marshes, attached bars, and overbank areas that can be inundated to create floodplains. The key components of conservation aquaculture management in the refugium are as follows: (1) no artificial feed is used, so that the fish develop the foraging strategies that will be needed in the wild and do not develop maladaptive behaviors associated with feeding; (2) the production of natural food organisms is based on indirect fertilization; (3) fish are subjected to managed predation, so that when stocked they are not behaviorally naïve; and (4) low stocking rates are used to mimic population densities in the wild. Results from 6 years of management and the lessons learned about facility design and conservation aquaculture management are discussed.