Seasonal changes, sea level rise, and global warming make flood events more frequent, which necessitates watershed management and efficient use of water resources. In this context, understanding the hydrodynamic behavior of basins is critical for the development of flood prevention strategies. The contributions of hydrological and hydraulic modeling techniques in this process are among the key determinants of sustainable water resources management. The Filyos Sub-Basin, located in the Western Black Sea Basin, stands out as one of the regions where flood risk assessment is a priority, as it has two important floodplains. This study aims to analyze the flood risk in the Filyos River Sub-Basin with hydraulic modeling methods, and to determine the Manning roughness coefficient. In the study, the parameters affecting the roughness of the river bed were analyzed using the Cowan method, and the effects of vegetation on river bed resistance were evaluated in the laboratory environment. Flood simulations were carried out for four different flow rates (Q1000, Q500, Q100 and Q50) using the HEC-RAS model, and the performance of flood protection structures were analyzed. The findings show that a significant portion of the existing protection structures are unable to meet the potential flood flows, which can cause serious damage to residential and agricultural areas. In basins with limited historical discharge data, such as the Filyos River, these findings provide important contributions to sustainable water resources management and regional planning processes. The results of the study serve as a reference for flood risk assessment, not only for the Filyos River Basin, but also for other basins with similar hydrodynamic characteristics. It is envisaged that future research, supported by larger data sets, can improve the accuracy of flood simulations. Furthermore, the Cowan method and HEC-RAS model used in this study are expected to contribute to strategic planning and engineering solutions to minimize flood risk in other watershed management projects. In future studies, we plan to further develop methodological approaches for determining the roughness coefficient, and to address applications to increase the effectiveness of flood protection structures.