Flood analyses when using a GIS-based integrated approach have been successfully applied around the world in large-sized watersheds. This study employed hydrological-hydraulic modeling to analyze flash floods by integrating HEC-HMS, HEC-RAS, and ArcGIS software for flood evaluation and control in a micro-watershed in the Samaru River, Nigeria. The watershed boundaries, its characteristics (soil and land use), the topographical survey, and the intensity duration frequency curve (IDF) of the study area were produced using data-driven techniques. The HEC-HMS model was used to derive the peak discharges for 2-, 5-, 10-, 25-, 50-, 100-, and 200-year return periods with the frequency storm method. Afterward, the water surface profiles for the respective return periods were estimated using the HEC-RAS hydrodynamic model. The simulated design flood for the 2-, 5-, 10-, 25-, 50-, 100-, and 200-year return periods at the reference location (the NUGA gate culvert) were 3.5, 6.8, 9.1, 12.1, 14.3, 16.6, and 19.0 m3/s, respectively, while those at the watershed outlet for the respective return periods were 7.5, 14.9, 20.3, 27.3, 32.6, 38.0, and 43.5 m3/s, respectively (with a water height of 0.9 m, 1.1 m, 1.3 m, 1.33 m, 1.38 m, 1.5 3m, and 1.8 m, respectively), at the NUGA gate culvert cross-section. The maximum water depths of about 0.9 m and 1.0 m were recorded in the right and left overbanks, which were similar to the simulated water depth for the 2- and 5-year return periods. Hence, for the smart control of floods passing through the river and major hydraulic structures, a minimum design height of 1.50 m is recommended. For the most economic trapezoidal channel section, a normal depth of 1.50 m, a bottom width of 1.73 m, a top width of 3.50 m, and a free board of 0.30 m is proposed to curb the overtopping of floods along the channel sub-sections. The findings of this study could help hydraulic engineers minimize flooding in streams and rivers overbanks in a micro-watershed.