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Study region: Marikina–Pasig basin, Philippines Study focus: A multiscale rainfall-runoff and inundation model was developed to simulate the severe flooding caused by a high-intensity short-duration storm rainfall event in the urban domain. The model used the 2D shallow-water flow and finite volume schemes with second-order space–time accuracy to automatically incorporate the runoff into the flood inundation. The adaptive mesh refinement scheme—a variable grid-sizing technique—was implemented to dynamically refine the mesh from a watershed-scale to a more precise inundation in a subcatchment floodplain. The digital terrain and surface models were used to represent the variations in flood propagation along buildings and artificial barriers in the urban area. Additionally, the simulated flood depths and extent were validated by comparison with the observed data. New hydrological insight: The severe inundation produced by the extreme rainfall event was perceived to be caused by a combination of fluvial and pluvial flooding; exacerbated by the domain’s flat and low-lying elevation and its geographical features acting as a flood water receiving catchment accrued from the adjacent mountainous regions. The proposed method can be used to identify the flood depth and water accumulation, estimated peak time, potential flash-flood prone areas, and imperceptible flood origins without the need to establish first the water level and stream discharge boundary conditions. The domain-specific flood simulations can be used for early warning and to identify a broader scope of possible evacuation points during storm-based flooding events.