Understanding hydro-sediment dynamics is critical to developing effective flood mitigation strategies in river basins with high sediment loads. This study aimed to assess the rainfall-runoff and sediment transport processes in the Santa Maria Watershed, Laguna, to identify flood hotspots. We employed the Rainfall–Sediment Runoff (RSR) model, which integrates a distributed rainfall–runoff model with a unit channel-based sediment transport model. The model was configured using watershed geomorphological data and validated using field-observed water levels and suspended sediment concentrations from September to December 2024. The simulation identified pronounced bed aggradation at two major meander bends in the plain area, highlighting these as potential high-risk sections for future flooding along the main river. Furthermore, the model identified the primary flood hotspots in agricultural lowlands away from the main river, caused by overflow from abandoned channels and a major tributary confluence. These results demonstrate that the RSR model is an effective tool for identifying flood hotspots linked to both sediment-driven geomorphological changes and complex topographic features. This is crucial for devising targeted mitigation strategies for vulnerable communities.

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