Isotope ratios and elemental concentrations in otoliths are often used as natural tags to reconstruct migratory movements and connectivity patterns in marine and anadromous fishes. Although differences in otolith geochemistry have been documented among geographically separated populations, inter-annual variation within locations is less frequently examined. We compared otolith isotope (δ 18 O and 87 Sr: 86 Sr) and elemental ratios (Sr:Ca and Ba:Ca) from several annual cohorts of juvenile American shad (Alosa sapidissima) in three rivers. These four geochemical signatures distinguished among river-specific populations of this species at both large and small geographic scales, with δ 18 O and 87 Sr: 86 Sr generating the majority of multivariate variation. We found significant variation among years for all variables in two to three rivers. However, the magnitude of variability differed among ratios, with δ 18 O ratios showing substantial inter-annual shifts while 87 Sr: 86 Sr ratios were relatively stable across years. Sr:Ca and Ba:Ca ratios also varied among years. These results imply that investigators using environmentally labile signatures must quantify geochemical signatures for each cohort of interest in order to confidently identify origins of migrants.