As a primary method for fluid conveyance, pipeline systems are critical infrastructure components, often installed adjacent to roadways due to practical constraints. The simultaneous presence of pipelines and hydraulic structures, such as culverts, significantly alters flow patterns and intensifies scouring processes, particularly during flood events. This synergy can undermine the stability of both the pipeline and downstream structures, potentially leading to severe consequences. Therefore, this study investigates the mechanism of scour induced by a pipeline positioned downstream of a culvert to propose effective protective measures and enhance system safety. Based on 216 experimental runs, this research examines scour around a pipeline under the influence of artificial bed roughness and unsteady flow conditions. Lowering the bed level, both with and without artificial roughness, resulted in a reduction of maximum scour depth, scour volume, and scour area, while concurrently increasing maximum deposition height, deposition volume, and deposition area. Specifically, by decreasing the bed level from 0 to −6 cm, the deposition volume increased by 251% in the absence of artificial roughness and by 318.4% in its presence. In both rough and smooth bed conditions, transitioning the pipeline from a buried state to an exposed state (above the bed) led to an increase in maximum deposition height, volume, and area. The maximum scour volume in both conditions was observed when the bed level was at zero, the pipeline was elevated above the bed, and positioned 9 pipe diameters downstream of the culvert. Increasing the distance between the pipeline and the culvert from 9 to 18 and 27 pipe diameters reduced scour volume by 28.4% and 29.2%, respectively, in the absence of artificial roughness, and by 17.7% and 18.2% in its presence. Finally, the installation of artificial roughness increased both scour volume and deposition volume by averages of 3.4% and 4.8%, respectively, while