Adding a new micro hydropower component to an established barrage, such as the Serayu Barrage in Central Java Province, poses significant structure risks and potentially compromises the stability of the structures. To mitigate these negative impacts, physical modeling was conducted at our hydraulic laboratory to accurately replicate 600 meters of the Serayu River, including the 110-meter-wide Serayu Barrage structure at a scale of 1:40. Multiple scenarios were examined to simulate hydrodynamic conditions and sediment transport along the barrage structure. Notably, downstream scouring conditions were identified as a crucial parameter affecting the structure’s stability. Results obtained using a design discharge of 2,470 m3/s revealed concerning findings, with an observed 4 to 6 meters deep scouring downstream near the end sill of the weir. Immediate mitigation measures using riprap are imperative to prevent further damage to the weir structure. This paper investigates several configurations for riprap protection to address the scouring problems. After implementing a full riprap arrangement downstream of the end sill, the scouring depth was reduced significantly and pushed far downstream. Looking at it from an economic standpoint, placing a full riprap configuration for downstream protection is a more financially efficient option over an extended period.