Floods frequently threaten villages near the Khazir River’s floodplains, causing crop losses and threatening residential areas. We used flood-related hydrological software, including WMS and HEC-HMS, to study this issue and determine how to reduce the recurrence of flooding. The software can be used to calculate a hydrograph of torrential flows in a river drainage basin and estimate the volume of torrential water and its flow rates on the Earth’s surface. The depth of rain has been evaluated and calculated in the SCS Unit Hydrograph for different return periods of 2, 5, 10, 20, 50, and 100 years. According to our study’s findings, the volume of the river’s drainage basin floods ranged between 29,680 and 2,229,200 m³, and the maximum flow value ranged between 10.4 and 66.4 m³/sec during various reference periods. To analyze and model the flood risks of the Khazir River, the HEC-RAS model was combined with the HEC-GeoRAS extension in ArcGIS. The floods were the focus of two study periods, 2013 and 2018, and were based on the digital elevation model and river discharge during the floods. According to the classification map of the flood depths, the areas of flood risk varied from low to very low (80.31%), medium (16.03%), and high to very high (3.8%). The analysis of the results revealed that the villages closest to the river’s mouth were more affected by the floods than other villages further downstream. HEC-HMS and HEC-RAS have been shown to have a strong correlation in evaluating flood risks and reliably forecasting future floods in the study area.