For riverine fishes threatened by fragmentation and flow modification, effective management requires an understanding of when and where key life history processes (spawning, recruitment and movement) take place. The structural and chemical properties of otoliths provide a unique means to recount a fish's life in time and space. We investigated the age structure of the migratory, pelagic-spawning golden perch (Macquaria ambigua) in the Murray River, Australia, and used water and otolith 87Sr/86Sr ratios to delineate the natal origin and movement of fish from discrete cohorts. Water 87Sr/86Sr was distinct among the Darling River (a major tributary) and lower and mid-Murray River. Otolith chemistry revealed golden perch collected in the lower Murray River were progeny of spawning in either the Murray or Darling rivers, during years characterised by within-channel rises in flow, or in both rivers in a year of overbank flooding. Movement of juvenile fish from the Darling River substantially influenced population structure in the lower Murray River, whereby post-flood population growth was largely due to the immigration of age-1+ fish. This study demonstrates the potential importance of tributary recruitment sources, dispersal and connectivity on main-stem population dynamics and the utility of otolith chemistry for spatially reconciling population structure and the life histories of freshwater fishes.