AbstractLarge rivers exhibit dynamic and complex geomorphic features, supporting some of the most biodiverse and ecologically productive ecosystems. However, their aquatic ecology is increasingly threatened by human modifications to natural channel morphology. The lack of systematic investigation and understanding of the interactions between hydrodynamics, water quality, and aquatic ecology within large‐scale, morphologically complex rivers has led to fragmented ecological management. This study investigates the large‐scale responses of fish communities to complex channel morphologies through two comprehensive field surveys of hydrodynamics, water quality, and fish distribution along a ∼30 km reach of the Yangtze River, encompassing channel narrowing, bifurcation, and the Yangtze River‐Poyang Lake cascading confluence system. Both surveys observed elevated fish densities at the confluence and narrowing section, particularly with a distinct Confluence Hydro‐Ecological Zone (CHEZ) within the post‐confluence channel, marked by a pronounced increase in fish density and species diversity relative to both upstream and downstream sections. Mixing dynamics driven by the confluence momentum ratio (Mr) regulate the CHEZ: slow mixing in the equivalent momentum regime (Mr ≈ 1) amplified the increase in fish density within the CHEZ, while rapid mixing in the unequal momentum regime (Mr >> 1) weakened such effect but expanded the CHEZ. Density of large fish was primarily influenced by water depth and water‐quality variability, whereas density of small fish was driven by seasonal population dynamics and hydrodynamic conditions. This study highlights that a comprehensive understanding of hydrodynamic configurations, water‐quality contrasts, and seasonal biological dynamics at confluences can inform process‐based strategies for sustainable river management.