<p>The geometry and deformation of river cross-sections play a crucial role in minimizing human and financial losses caused by flooding. To obtain geometric parameters on cross-sections and hydraulic conditions of the flow, the need for hydraulic modeling is inevitable. In this study, hydraulic simulation was performed using HEC-RAS software on the Zayandehrud River in Iran. To determine the optimal river cross-section geometry, the Secretary Bird Optimization Algorithm (SBOA) was implemented as a novel simulation-optimization approach. This approach aimed to achieve a maximum dredging volume while maintaining hydraulic stability during the 25-year flood. Then, the new Optimum Cross-section Indices (OCIs), which display the numerical value of the river cross-section according to its optimal condition, were used to evaluate river cross-sections in their optimal state. To validate these indices and the watercourse, geometric parameters like width, depth, and area were measured and analyzed at 12 stations within a 91-kilometer stretch. Based on the results, the optimized depth, area, and volume increased rather than the simulated ones towards the downstream. The OCIs values ranged from 8% to 80%, reflecting an increasing requirement for channel enhancement toward the downstream reaches. The optimization approach proved highly effective, enhancing the river’s watercourse capacity by 21.08% post-optimization. Furthermore, the results underscore the superiority of SBOA by 1.51% and 6.85% in comparison with the Red Fox Optimization (RFO) and Teaching Learning-Based Optimization (TLBO) algorithms, respectively. These results illustrated a practical approach for river management and optimization.</p>