Urban flooding is becoming increasingly destructive in the Mediterranean region as more and more urban infrastructure and socioeconomic activities are exposed to flood risk. The metropolitan area of Athens, Greece, is no exception to this flood-prone regime, presenting a rich record of flood events during the last century. On 22 February 2013, a high-intensity storm that lasted 7 hours hit Athens, severely impacting the transportation sector, hindering vehicle circulation and the overall performance of the road network. This paper studies the impact of high intensity storms in urban areas by examining the effects of the February 2013 Athens storm and the resultant flood event. Its novelty lies in the impacts quantification approach, applying cutting-edge traffic flow control methodologies in the form of Macroscopic Fundamental Diagrams. It quantifies the storm's impacts on vehicular traffic in terms of operational disruptions during the event by analyzing various traffic-related indicators, such as travel time, delays, speed drop and re-routing of vehicles, using data from the Athens traffic management center and urban freight vehicle fleets. Results show increased travel times, significant changes in routing and substantial speed drops, highlighting the disruptive effects of the flooding event on traffic. The importance of developing a qualitative and quantitative understanding of the effects of such events in urban areas is particularly high considering the context of the changing climate and the increasing frequency of extreme weather events.