Juvenile habitat use and early life migratory behaviors of successfully recruited adult fish provide unique insight into critical habitats for a population, and this information allows restoration plans to be tailored to maximize benefits. Retrospective analysis of adult otolith chemistry combined with fish-otolith growth models were used to assess juvenile nursery habitat selection and size at egress to adult habitats (marine waters) for anadromous alewife and blueback herring from 20 rivers throughout the eastern US. Between-species differences in the size of emigrants were small, with blueback herring found in freshwater nurseries ~ 8% more frequently than alewives, and alewives using a combination of freshwater and estuarine nurseries ~ 9% more than bluebacks. Estuarine nursery use was more common in populations at lower latitudes. No clear trends in sizes of emigrants or habitat use were observed between the species in watersheds where both co-occur. Principal component analysis of latitude, watershed area, estuary area, accessible river kilometers, and percentage of the watershed in urban use indicated that the combined effects of these watershed characteristics were correlated with size at egress. These results highlight the considerable plasticity in early life habitat use among populations of anadromous fishes as well as the effect of watershed characteristics on early life migration timing and strategies.