Floods are a natural phenomenon that cause damage to structures and property as well as negatively affect human life. Assessing the extent, speed, power, and depth of flooding has always been a challenge for water resource planners. This research developed a hydraulic simulation model for the Cubanicay and Bélico urban rivers embedded in the city of Santa Clara, Cuba. The methodology was based on a one-dimensional model of the Hydrological Engineering River Analysis System (HEC-RAS) and GIS-based methods. The HEC-RAS model (Beta) and three modeling flood tests for scenarios of 1% (100 years), 2% (50 years), and 10% (10 years) of probability for hydrometeorological events were analyzed. Bank lines, flow path lines, and cross-section cut lines were extracted from Digital Elevation Models. Manning’s roughness coefficients were considered for the channel morphology and soil typology. The flood Beta model results were accurate with a difference of ±0.10 m considering the water footprint found in the field. The results showed that the areas near the control section 2 + 87 presented a high risk of flooding. The flood limit map for urban areas could be an important tool for researchers, planners, and local governments for risk assessment and to develop evacuation plans and flood mitigation strategies in order to reduce human and economic losses during a flood.