This paper develops a method integrating Geographic Information Systems (GIS) and the Decision-Making Trials and Evaluation Laboratory (DEMATEL) for the analysis of factors influencing urban flood risk and the identification of flood-prone areas. The method is based on nine selected factors: land use/land cover (LULC: the ratio of built-up areas, the ratio of greenery areas), elevation, slope, population density, distance from the river, soil, Topographic Wetness Index (TWI), and Normalized Difference Vegetation Index (NDVI). The DEMATEL method is used to determine the cause–effect relationship between selected factors, allowing for key criteria and their weights to be determined. LULC and population density were identified as the most important risk factors for urban floods. The method was applied to a case study—the Serafa River watershed (Poland), an urbanized catchment covering housing estates of cities of Kraków and Wieliczka frequently affected by flooding. GIS analysis based on publicly available data using QGIS with weights obtained from DEMATEL identified the vulnerable areas. 45% of the total catchment area was classified as areas with a very high or high level of flood risk. The results match the actual data on inundation incidents that occurred in recent years in this area. The study shows the potential and possibility of using the DEMATEL-GIS method to determine the significance of factors and to designate flood-prone areas.