Understanding multiple challenges that restrict conservation success is a central task of applied ecology, especially when resources are limited and actions are expensive, such as with reintroduction programs. Simultaneous consideration of multiple hypotheses can expedite identification of factors that most limit conservation success. Since 2001, reintroduction of a migratory population of Whooping Cranes (Grus americana) has been under way in eastern North America. Hatching success, however, has been extremely low. In our study area, in and near Necedah National Wildlife Refuge in central Wisconsin, USA, we simultaneously tested 3 hypotheses explaining poor hatching success: harassment of incubating birds by black flies (Simuliidae), effects of captivity, and inexperience of breeders. When black flies were experimentally suppressed, hatching probability doubled. Daily nest survival for Whooping Cranes was strongly and negatively related to an index of black fly abundance, particularly of Simulium annulus. Daily nest survival was negatively but only weakly related to the number of generations that ancestors of breeding Whooping Cranes had been in captivity and was not related to nesting experience. We also examined whether Whooping Cranes were nesting later to avoid stress from black flies. Phenology shifted earlier with more growing degree days and greater nesting experience and was only weakly related to year. Overall, improved hatching success did not lead to better reproductive success. Although effects of black flies on hatching success can be mitigated through management, such actions would not be adequate to generate satisfactory population growth. Recognition of this limitation was hastened through experimentation.