Flooding causes serious loss of life and property, especially in highly urbanized regions. The driving mechanisms of flooding should be investigated in detail and permanent precautions should be taken. One of the latest fatal events occurred in Ayamama River in Istanbul on September 9, 2009. As a result of this flood, 32 people died and 50 people were injured. In addition, many structures were damaged, which influenced the economy significantly. In this study, a hydrodynamic model of the watershed was generated by using the Watershed Modeling System (WMS) (version 9.1) and the US Environmental Protection Agency's Storm Water Management Model (EPA SWMM) (version 5) in light of observations after the September 2009 flood event. The flood depth and volume belonging to the flood event were calculated using the EPA SWMM model. In addition, the flood hazard map was produced using the WMS. The validation of the models was made based on field observations and event reports. The results obtained by the two models showed that the flood depth reached approximately 11m at the critical regions, which are highly prone to flooding on the Ayamama watershed. Moreover, the flood extent reaches about 1,200m downstream of the watershed. The related flood hazard map was produced and assessed to predict future events and flood management. Moreover, the capabilities of the two different computer models are evaluated by comparing the output of the models. It is concluded that an especially high number of constructions of the floodplain in Ayamama region act as a big threat on flooding.