Natural hazards due to climate change have become the new norm in our cities. These events show the vulnerabilities of our cities to extreme conditions, mainly displayed as flash wadi flooding as a result of a short duration of intensive and eroded its shoreline along the coast, resulting in huge impacts, including human losses and urban and infrastructural damages. This study used the urban flood risk mitigation model through an open-source tool—Integrated Evaluation of Ecosystem Services and Trade-off (InVEST)—to estimate the amount of runoff due to two extreme rainfall events for each watershed considered. We used a digital shoreline analysis system (DSAS) to quantify the Al Khaboura shoreline erosion as a result of Shaheen’s storm surge. With the DSAS, the model showed that, during the short period of the event, the Al Khaboura coastal line was eroded by 16.33 m/y, representing 7.82% of its coastal line, up to a maximum erosion distance of 1428.5 m. The weighted linear regression showed the average mean rate of shoreline change of 6.79 m/y. These models could provide a clear picture of the city vulnerability to allow us to propose a corrective measure for interventions at local and regional scales.