The management of anadromous fishes is inherently complicated as this suite of species exhibits complex life-histories in multiple habitats and is subject to varying natural and anthropogenic influences during discrete ontogenetic periods. Life-history based simulation models have been increasingly adopted by fishery scientists and managers to help understand potential effects of management decisions on fish populations while incorporating uncertainty in life-history, climate, and other components of resource management systems. We applied one such model to Blueback Herring Alosa aestivalis in the Hudson River watershed, NY, USA. Our goal was to better understand influences of historical habitat loss on anadromous fishes and determine to what extent and under what conditions novel habitat created by canal infrastructure might confer increased population abundance. We found that access to historical habitat in the upper Hudson River increased population abundance at all upstream dam passage rates with sufficient downstream survival of adult and juvenile Blueback Herring, but that abundance decreased with increasing upstream passage relative to the “no passage” scenario when downstream survival through dams was not sufficiently high. Access to novel spawning habitat in the Mohawk River canal system resulted in increased abundance of Blueback Herring when downstream survival of adults and juveniles was at least 0.80 per dam and both upstream passage and probability of using the Mohawk River were both greater than about 0.25. Both mortality during upstream passage of locks in the Mohawk River and marine fishery mortality had the potential to reduce Blueback Herring abundance below historical population abundance despite access to novel spawning habitat. These results highlight the complexity associated with effects of upstream and downstream fish passage standards on population responses while emphasizing similarities observed in other diadromous species and watersheds.