This paper presents an integrated approach to simulate flooding and inundation for small- and medium-sized coastal river basins where measured data are not available or scarce. By coupling the rainfall–runoff model, the one-dimensional and two-dimensional models, and the integration of these with global tide model, satellite precipitation products, and synthetic aperture radar imageries, a comprehensive flood modeling system for Tra Bong river basin selected as a case study was set up and operated. Particularly, in this study, the lumped conceptual model was transformed into the semi-distributed model to increase the parameter sets of donor basins for applying the physical similarity approach. The temporal downscaling technique was applied to disaggregate daily rainfall data using satellite-based precipitation products. To select an appropriate satellite-derived rainfall product, two high temporal-spatial resolution products (0.1 × 0.1 degrees and 1 h) including GSMaP_GNRT6 and CMORPH_CRT were examined at 1-day and 1-h resolutions by comparing with ground-measured rainfall. The CMORPH_CRT product showed better performance in terms of statistical errors such as Correlation Coefficient, Probability of Detection, False Alarm Ratio, and Critical Success Index. Land cover/land use, flood extent, and flood depths derived from Sentinel-1A imageries and a digital elevation model were employed to determine the surface roughness and validate the flood modeling. The results obtained from the modeling system were found to be in good agreement with collected data in terms of NSE (0.3–0.8), RMSE (0.19–0.94), RPE (− 213 to 0.7%), F1 (0.55), and F2 (0.37). Subsequently, various scenarios of flood frequency with 10-, 20-, 50-, and 100-year return periods under the probability analysis of extreme values were developed to create the flood hazard maps for the study area. The flood hazards were then investigated based on the flood intensity classification of depth, duration, and velocity. These hazard maps are significantly important for flood hazard assessments or flood risk assessments. This study demonstrated that applying advanced hydrodynamic models on computing flood inundation and flood hazard analysis in data-scarce and ungauged coastal river basins is completely feasible. This study provides an approach that can be used also for other ungauged river basins to better understand flooding and inundation through flood hazard mapping.