Fish population dynamics are influenced by intrinsic and environmental drivers across multiple spatial and temporal scales. A thorough understanding of these drivers is essential for maintaining fish recruitment in flow-regulated rivers. In the Murray-Darling Basin (MDB) in Australia, golden perch (Macquaria ambigua) are an iconic species with a life history characterised by irregular, strong recruitment of year classes. In-channel flow pulses and overbank flows are important for spawning and recruitment; however, the drivers of fluctuations in golden perch recruitment have not been sufficiently quantified to allow for full operationalisation into river and fishery management. We used long-term standardised electrofishing data to model relationships between the relative abundance of young-of-the-year (YOY) golden perch with large-scale climate indices, local river hydrology and temperature, and river/fishery management actions. While consistent recruitment was observed in only five rivers, there were strong, positive associations between the abundance of YOY golden perch and two broadscale climatic drivers (Australian Monsoonal Index and total rainfall across the northern MDB). The driver of these relationships is likely to be the effects of climate on local river discharge and temperature. YOY abundance increased with temperature and generally increased with river discharge to an optimum before declining at a very high discharge. We also found positive but variable effects of stocking, suggesting that stocking of fish can augment natural populations but that outcomes are spatially and temporally inconsistent. Our results have the potential to enable proactive management targeted towards supporting the hydrological conditions necessary for self-sustaining golden perch populations.