Floods are amongst the most frequent and destructive type of disaster, causing significant damage to communities. Globally, there is an increasing trend in the damage caused by floods generated by several factors. Flooding is characterized by the overflow of water onto dry land. Tropical cyclones generate floods due to excess water in rivers and streams and storm surges; however, the hazard of both phenomena is presented separately. In this research we present a methodology for the estimation of flood hazards related to tropical cyclones, integrating runoff and storm surge floods. As a case study, we selected the south-western suburbs of the city of La Paz, the capital of the state of Baja California Sur in northwest Mexico. The city has experienced in recent years an expansion of the urban area. In addition, there is an infrastructure of great importance such as the transpeninsular highway that connects the capital with the north of the state, as well as the international airport. Our results indicate that urban areas, agricultural lands, as well as the air force base, airport, and portions of the transpeninsular highway are in hazardous flood areas, making necessary to reduce the exposure and vulnerability to these tropical cyclone-related events. A resulting map was effective in defining those areas that would be exposed to flooding in the face of the impact of tropical cyclones and considering climate change scenarios, which represents an invaluable source of information for society and decision-makers for comprehensive risk management and disaster prevention.