Anabranching river systems, characterized by multiple stable channels separated by vegetated islands, play a crucial role in maintaining aquatic biodiversity. Despite their ecological significance, anabranches' influence on ecohydraulic environments and fish habitats remains largely unexplored. This study seeks to address the gap by offering an in-depth investigation into the habitat dynamics and sensitivity of anabranching rivers, aiming to enhance the understanding of anabranches’ ecological suitability, resilience, and stability. For this purpose, the study establishes an ecohydraulic framework to assess the habitat status for target species in four anabranching reaches with distinct channel complexity. The main channels provide optimal habitats for species favoring dynamic environments at moderate to high flows. In contrast, the low-energy anabranches provide refuges during extreme flows, supporting species that rely on stable and low-velocity conditions. The study also highlights the critical role of channel complexity in sustaining ecological resilience; reaches with complex anabranching patterns and vegetated islands provide higher habitat stability across a wide range of hydrological scenarios, mitigating the impacts of extreme events on aquatic habitats. Long-term ecological predictions demonstrate that anabranching channels enhance ecological stability, with limited fluctuations in habitat quality. From a management perspective, this study advocates for conservation practices that preserve these multi-channel structures and hydrological connectivity, supporting sustainable habitat conditions under changing environmental pressures. This research offers valuable insights for managing anabranching rivers and contributes a framework for habitat assessment applicable to similar ecosystems.