We investigated the merits of performing multi-scale flood simulations with nested two-dimensional flood simulation models for flood risk management applications over an extended period with infiltration and evapotranspiration. For nested calculations, 1) inter-district, 2) district, and 3) regional scales were arranged as three levels in the nested model. Because the nested method can be useful for flat land, the Gaibandha District in Bangladesh was chosen for the study area. This area is a typical flood prone area that is inundated frequently by flood flow from the Jamuna River. First, we performed a year-round flooding simulation for the year 2007 by focusing on a monsoon flood, and validated the results via satellite images. Second, we evaluated the differences of floods in the case of 2.33- and 100-year return periods by using discharge data produced by a flood frequency analysis. We successfully simulated the flooding in each nested level for 2007, and this enabled us to evaluate the flood risks at different scales. In addition, we delineated the flood extent for different return periods and clarified the relationship between the peak water level of the river and the flood extent. The nested method proved to be advantageous because its implementation is not computationally demanding.