Duran is a coastal city located in the Guayas Estuary region in which 24% of urban sectors suffers from the effects of chronic flooding. This study seeks to assess the causes of Duran’s vulnerability by considering exposure, population sensitivity and adaptive capacity to establish alternatives to reduce its vulnerability to flooding. An operational framework is proposed based on the vulnerability definition of the Intergovernmental Panel on Climate Change (IPCC) and applying a census-based Index of Vulnerability, a geographic information system and local knowledge of urban development. A Principal Component and equal weighting analysis were applied as well as a spatial clustering to explore the spatial vulnerability across the city. A total of 34% of the city area is mapped as having high and very high vulnerability, mostly occupied by informal settlements (e.g., 288 hectares). Underlying factors were poor quality housing, lack of city services and low adaptive capacity of the community. However, some government housing programs (e.g., El Recreo), with better housing and adaptive capacity were also highly vulnerable. Limited urban planning governance has led to the overloading of storm water and drainage infrastructure which cause chronic flooding. Understanding the underlying causes of vulnerability is critical in order develop integrated strategies that increase city resilience to climate change.