This study aimed to calculate and analyze total overflows that accumulate in urban manholes in the target drainage basin of Samsung-dong, Seoul in heavy rainfall events with different temporal distribution characteristics, using the EPA’s Storm Water Management Model (EPA-SWMM model). Inundation behaviors were analyzed using the two-dimensional flood model (FLO-2D). The extreme rainfall events were produced using different exceedance probability Huff distributions for different durations and return periods, such as from 1 to 3 h and 10 years, 50 years, 80 years, 100 years, respectively. The inundation model was validated using the actual flood observations on 21 September 2010 in the Samsung-dong drainage basin. The total overflow amount showed considerable differences according to the different time distribution characteristics, such as the temporal location of the storm peak and the concentration level of the storm. Furthermore, the inundation behaviors were also related to the temporal characteristics of storms. The results illustrated that the consideration of the temporal distribution characteristics of extreme rainfall events is essential for an accurate understanding of the rainfall–runoff response and inundation behavior in urban drainage basins.