Water resource management and extensive irrigation infrastructure have fundamentally altered natural flow regimes, with significant implications for the productivity of downstream aquatic ecosystems. To evaluate these impacts, it is common to use river discharge as a proxy for the environmental conditions driving fish growth. I developed a Generalised Additive Mixed Model (GAMM) to quantify the influence of ontogeny, habitat residency, and river discharge on the somatic growth of barramundi (Lates calcarifer) in the heavily regulated Burdekin River basin, Australia. I used otolith microchemical signatures (Sr:Ca) and otolith increment widths to infer their habitat-use histories and reconstruct individual growth rates. The resulting model was applied to simulated hydrological scenarios to compare growth potential under modern ("Current") versus natural ("Pre-Development") flow conditions. The GAMM robustly explained 84.4% of the total variance in somatic growth. Counterintuitively, the model revealed a complex and often negative relationship between wet-season river discharge and growth, across all life-history strategies. Scenario testing indicated a perverse outcome: predicted barramundi growth potential was significantly higher under the reduced flow rates of the current flow regime than under the simulated natural scenario. These findings suggest that in heavily modified landscapes, main-channel discharge may become decoupled from the fine-scale hydrology of the adjacent floodplains where juvenile fish forage. ts. To accurately predict ecological health and productivity, future fisheries models in regulated systems should incorporate off-river floodplain hydrology rather than relying solely on primary channel gauges.