Urban floods from thunderstorms cause severe problems in Metro Manila due to road traffic. Using Light Detection and Ranging (LiDAR)-derived topography, flood simulations and anecdotal reports, the root of surface flood problems in Metro Manila is identified. Majority of flood-prone areas are along the intersection of creeks and streets located in topographic lows. When creeks overflow or when rapidly accumulated street flood does not drain fast enough to the nearest stream channel, the intersecting road also gets flooded. Possible solutions include the elevation of roads or construction of well-designed drainage structures leading to the creeks. Proposed solutions to the flood problem of Metro Manila may avoid paralyzing traffic problems due to short-lived rain events, which according to Japan International Cooperation Agency (JICA) cost the Philippine economy 2.4 billion pesos/day.