Effective flood management requires a comprehensive understanding of interactions between multiple flooding sources. This study investigates compound flooding in the Brisbane River Estuary (BRE), Australia, using the MIKE 21 hydrodynamic model to assess the combined effects of tidal and riverine processes on flood extent and water levels. Unlike conventional studies that evaluate these factors separately, this research quantifies the impact of boundary condition variations at the Moreton Bay entrance on flood modelling accuracy. The model was calibrated by adjusting Manning’s n, achieving a Nash–Sutcliffe efficiency (E_ns) ranging from 0.84 to 0.95. Validation results show a 90% agreement between the simulated and observed 2011 flood extent. The findings highlight the critical role of tidal boundary conditions, as their exclusion led to a 0.62 m and 0.12 m reduction in flood levels at Jindalee and Brisbane City gauges, respectively. This study provides valuable insights for improving flood risk assessment, model accuracy, and decision-making in estuarine flood management.