Flooding in urban river catchments is an increasing concern, especially in areas exposed to both riverine and coastal hazards. This study evaluates flood mitigation strategies for the Antiao River Catchment in the Philippines using integrated hydrologic and hydraulic modeling (Hydrologic Engineering Center—Hydrologic Modeling System [HEC-HMS] and Hydrologic Engineering Center—River Analysis System [HEC-RAS]). Three scenarios were assessed: (1) a baseline “Do-Nothing” case, (2) conventional flood protection dikes (FPDs), and (3) a hybrid approach combining FPD with nature-based solutions (NbSs), including reforestation, mangrove restoration, and constructed wetlands. Model validation showed strong agreement with national flood hazard maps and empirical peak-flow estimation methods. Results indicate that while FPD reduces flood extent, it can increase localized flood depths and water surface elevations due to flow confinement. The integrated FPD-NbS approach was associated with lower flood depths, reduced flow velocities, and moderated water surface elevations relative to the FPD-only scenario, indicating improved hydraulic performance under extreme flood conditions. These findings support the use of combined structural and nature-based interventions to enhance urban flood resilience in river catchments influenced by both fluvial and coastal processes.