This study presents a geographic information system (GIS)-supported three-dimensional fuzzy risk assessment approach (3D GIS-FRA) for flood risk assessment that is based on the development of a fuzzy-set risk model, 3D GIS mapping, and a hydro-statistical simulation. Using GIS and a digital elevation model (DEM), urban settings under different levels of flood risk are visualized and hydraulic simulations conducted for various river flow scenarios to determine the flow rates for specified risk levels. Then, a statistical analysis is carried out using historical records to establish a set of risk criteria that consider critical factors that affect the peak flow rate. Finally, the developed fuzzy-set risk model is applied to examine the flood risks using the outputs from the hydraulic models and statistical analysis. The developed method is applied to a section of the Red River in Southern Manitoba, Canada. The 3D GIS-FRA results indicate that there is a possibility of having a highly risky situation for the upper-bound extreme condition for the study area, although only limited impacts are expected for a 25-year flood. For the 75-year flood scenario, the overall flood risk level is high for the whole area. The results indicate that the developed risk analysis system is useful for systematically quantifying the flood risks and the related system uncertainties.