The chemical information stored in otoliths reflects individual lifetime variations in growth, movements, and responses to environmental conditions, providing a multifaceted approach to unravel connectivity patterns in fish populations. When combined with genetic markers, these data can bridge individual life histories with broader patterns of gene flow. Here, we employ a multi-disciplinary approach to unravel the complexities in the connectivity of estuarine fish. We integrate single-Nucleotide polymorphisms (SNPs), otolith shape, isotopic and elemental composition to provide a comprehensive assessment on population structure, lifetime migrations and multigenerational connectivity of Acantopagrus butcheri across southern Australia. Otolith chemical information confirmed variations in movement patterns for this partial migrant species, reflecting diverse environmental histories within and across estuaries. Despite evidence of movement between estuaries and coastal areas, genetic markers reveal population structuring at small spatial scales, highlighting estuarine dependency and limited gene flow even among nearby estuaries. Overall, we highlight, how otolith-derived chemical information combined with genetic markers provide critical insights into the spatial scales of movement and gene flow, offering a clearer understanding of population dynamics and connectivity.