The development of numerical models to simulate the real time situations is important to find possible solutions for natural disasters. Numerical models can also evaluate the effectiveness of the possible solutions by analyzing various scenarios. Coupled 1D and 2D hydraulic models play a significant role in analyzing flooding problems. Kubokawa, Japan had undergone flooding in 2014. We developed a detailed flood inundation model incorporating the available pumps, flood gates and other components in order to analyze possible countermeasures for mitigation of floods in the future. The model includes rainfall runoff models, a 1D river model and a 2D river basin model. The developed model was verified using field observation data of high water levels in the river and the inundations of the area. The results from the numerical model and field survey data indicate that the main causes for the flooding are the bathymetry of the area (i.e., the low lying areas in the surrounding high elevations) and the flow from the surrounding mountain. It was also found that the river has not overflowed. In this study, several countermeasures were identified to potentially mitigate future flooding. They include constructions of two retention ponds and a bypass channel for the inflow from surrounding mountain area. This paper summarizes the development of numerical model and the analysis performed to evaluate the effectiveness of such flood mitigation measures. The results indicate that the construction of bypass channel with two retention ponds can reduce the maximum inundation volume by 38% and the inundated area greater than 0.5 m depth by 26 %.