Flooding has been widely regarded as the most destructive natural hazard, causing significant disruptions in transportation. While previous empirical observations focused on the effects of rainfall on traffic, they often overlooked the direct impact of flooding on urban transportation systems. This study addressed this gap by investigating the effects of flooding on traffic flow in Metro Manila. By analyzing 15 roads under various flood conditions, the study developed empirical relationships between flood depth and key traffic parameters. The findings revealed significant reductions in road capacity and vehicle volume as flood depth increased. New polynomial functions were developed to model the relationship between flood depth and average vehicle speed for different road types. Moreover, the effects of flood-induced lane closures on road capacity were also highlighted. These insights led to the modification of Volume-Delay Functions (VDFs) to incorporate flood-related factors, enhancing the accuracy of traffic predictions during flood events. The research provided a foundation for improved flood-based transportation within Metro Manila, with potential applications in other flood-prone urban areas globally.