Box culverts are utilized in situations where natural stream flow intersects with roads and railway lines. This research utilizes a digital elevation model and the water Modeling System software to assess the catchment area of the primary valley and identify the factors contributing to flooding in Qoshtapa City. The study involves an analysis of the existing culvert and generated the necessary data for the design of a new culvert. Despite the presence of the existing culvert, floodwater levels rose to over 1 m above the roadway elevation of Erbil-Kirkuk during the last flood event in 2021–2022. The research collected hydrological and climatic data for the study area, conducted soil type analysis using the Harmonized World Soil Database software, and performed hydraulic calculations to estimate the maximum flood discharge of the valley using the Hydrological Engineering Center-Hydrological Modeling System software for flood return periods of 50, 100, and 200 years, for design, to select the best economic alternative. The new culvert design was executed using Bentley Culvert Master software to ensure that floodwaters can flow through the culvert without rising to street level. The results indicated that the new culvert design surpasses the capacity of the existing one. The results show that the best economic alternative hydraulic design is the first alternative capacity of 201 m3/s of a 100-year return period; the new design cross-section area of the culvert is 52.5 m2.