An understanding of population demographics and life history processes is integral to the rehabilitation of fish populations. In Australia’s highly modified Murray–Darling Basin, native fish are imperilled and fish deaths in the Darling River in 2018–19 highlighted their vulnerability. Golden perch (Macquaria ambigua) is a long-lived percichthyid that was conspicuous in the fish kills. To guide population rehabilitation in the Darling River, pre-fish kill age structure, provenance and movement of golden perch were explored using otolith microstructure and chemistry (87Sr/86Sr). Across the Lower and Mid-Darling River, recruitment was episodic, with dominant cohorts associated with years characterised by elevated discharge. There was substantial variability in age structure, recruitment source and movement patterns between the Lower and Mid-Darling River. In the Mid-Darling River, tributaries were an important recruitment source, whereas in the Lower Darling fish predominantly originated in the Darling River itself. Downstream movement of juveniles, upstream migration of adults and return movements to natal locations were important drivers of population structure. Restoring resilient golden perch populations in the Darling River will be reliant on mitigating barriers to movement, promoting a connected mosaic of recruitment sources and reinstating the hydrological and hydraulic factors associated with spawning, recruitment and dispersal. Globally, increasing water resource development and climate change will necessitate such integrated approaches to the management of long-lived migratory riverine fishes.