Flow discharge and anthropogenic activities influence the composition and configuration of habitat patches in river ecosystems. Understanding the response of habitat landscapes and the corresponding fish habitat quality is crucial for river management. We investigated the reaction of fish habitat suitability and variant flow discharge performance in examining aquatic habitat patch fragmentation. The hydraulic simulation and fish habitat calculation were used to determine the flow characteristics, habitat conditions, and river landscapes. FRAGSTATS was applied to explore the composition and configuration of habitat patches. Cluster analysis and logistic regression were employed to compute the spatiotemporal variabilities of riverscape indices and establish the relationship between riverscape attributes and fish habitat quality. The results indicate that the changes in specific habitat features are associated with the riverscape indices of total edge (TE), mean nearest-neighbor distance (MNN), interspersion and juxtaposition index (IJI), mean patch size (MPS), and area-weighted mean patch fractal dimension (AWMPFD). The flow discharge is the key to determining habitat fragmentation in rivers, with natural barriers occurring at low flow. In contrast, weirs are anthropogenic obstacles that have significant adverse effects on the downstream corridor. A priority restoration activity to conserve river habitat is to create refuge pools during dry seasons by modifying channel morphology. The positive correlation between habitat suitability and MPS and the negative relationship between habitat suitability and AWMPFD highlight the patch size and shape complexity that are critical indices for pool creation. The prediction of the landscape attributes of the outcomes under different scenarios could support the decision-making in river management. The innovative integrated method presented in this study provides a solid foundation and supports the implementation of nature-based solutions for sustainable river management. Display omitted •A novel river habitat management model for fish was established.•Changes with the specific habitat features are evidenced with the riverscape indices.•Low flow discharge and weirs disconnect habitat patches and disrupt river corridors.•Restoration priority is to create refuge pools for endemic fishes during dry seasons.•Patch size and shape complexity are the critical indices for the pool creation.