Native aquatic species are in decline, and hatcheries can play an important role in stemming these losses until larger ecological issues are addressed. However, as more federal and state agencies face budget uncertainty and the number of imperiled species increases, it is necessary to develop a tool to prioritize species for conservation propagation. Our objective was to create prioritized lists of aquatic species that may benefit from conservation propagation for five states in the United States. Biologists developed an influence diagram and provided information for multiple attributes affecting prevalence of species. The influence diagram and information for each species was used in a Bayesian belief network to generate a score to prioritize propagation of a species and the feasibility of propagation. When all taxa were ranked together within a state, mussels, amphibians, and a crustacean were included among fishes in the top species that may benefit from propagation. We recognize that propagation is one tool for conservation of imperiled species and that additional factors may need to be addressed to ensure species persistence. Nevertheless, we contend our quantitative approach provides a useful framework for prioritizing conservation propagation.