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ABSTRACT ObjectiveEstuarine fishes experience significant diel and seasonal variations in their environments, with climate change introducing additional stressors, including altered salinity, temperatures, and water levels. American Eels Anguilla rostrata are present in Atlantic estuaries from Venezuela to Greenland. Despite their wide distribution and shrinking population, American Eels are understudied, in part because of the research challenges posed by their unusual catadromous life history. This study examines the spatial effects of changing estuarine water quality variables (water temperature, dissolved oxygen, and salinity) on the American Eel population in the Hudson River estuary (HRE). MethodsThe Hudson River Biological Monitoring Program, conducted from 1974 to 2017, consists of a suite of surveys recording fish abundance data and water quality variables. As the largest component of the Hudson River Biological Monitoring Program, the Long River Ichthyoplankton Survey contains 44 years of data on American Eels in the HRE. Using LRS catch data and Hudson River Biological Monitoring Program water quality measurements, we developed statistical models of American Eel population centers in the HRE. ResultsThe young-of-year and yearling-or-older population centers shifted downstream over the course of the Long River Ichthyoplankton Survey at average rates of approximately 1.1 and 0.41 km per year, respectively, despite higher temperatures and lower dissolved oxygen conditions closer to the estuary’s mouth. Mean water temperature and dissolved oxygen for the entire estuary have significant relationships with the population centers of both age-classes, although the eels were not apparently tracking stable conductivity or water temperature conditions; nor were the young of year tracking stable dissolved oxygen levels. ConclusionsThe downstream shift in HRE American Eel population centers over several decades and the relationship between this shift and changing environmental conditions indicate the need for improved understanding of the population dynamics of the globally distributed and declining species of the genus Anguilla. This knowledge is critical in the face of rapidly changing ecosystems.