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A physically-based, distributed-parameter hydrologic model was used to simulate a recent flood event in the city of Hafr Al Batin, Saudi Arabia to gain a better understanding of the runoff generation and spatial distribution of flooding. The city is located in a very arid catchment. Flooding of the city is influenced by the presence of three major tributaries that join the main channel in and around the heavily urbanized area. The Integrated Multi-satellite Retrievals for Global Precipitation Measurement Mission (IMERG) rainfall product was used due to lack of detailed ground observations. To overcome the heavy computational demand, the catchment was divided into three sub-catchments with a variable model grid resolution. The model was run on three sub-catchments separately, without losing hydrologic connectivity among the sub-catchments. Uncalibrated and calibrated satellite products were used producing different estimates of the predicted runoff. The runoff simulations demonstrated that 85% of the flooding was generated in the urbanized portion of the catchments for the simulated flood. Additional model simulations were performed to understand the roles of the unique channel network in the city flooding. The simulations provided insights into the best options for flood mitigation efforts. The variable model grid size approach allowed using physically-based, distributed models-such as the Gridded Surface Subsurface Hydrologic Analysis (GSSHA) model used in this study-on large basins that include urban centers that need to be modeled at very high resolutions.