Sand traps in irrigation networks are typically used in mitigating canal sedimentation. In irrigation networks located in basins of high sediment yield due to the presence of volcanoes, it is essential to assess the vulnerability of sand traps. Using sediment yield at irrigation scheme inlets, sand trap vulnerability can be evaluated. This study aims to understand the vulnerability of irrigation sand traps throughout the Progo–Opak–Serang (POS) Volcanic River Basin, Indonesia, via mapping the sediment yield distributions in the basin. We employed the Revised Universal Soil Loss Equation to estimate soil loss, where the results show that the average soil loss in the POS River Basin is 179.69 tons/ha/year that falls under the category of moderate erosion potential, while the average sediment yield for the whole basin is 51.04 tons/ha/year. Parts of the basin with high yields of more than 180 tons/ha/year were mostly found along the volcanic mountains such as Sindoro, Sumbing, Merapi, Merbabu, and Telomoyo, and the Menoreh Hills. The model demonstrated relatively high performance with R2, NSE, RMSE, and MAE of 0.89, 0.82, 0.14, and 0.11, respectively. Within the POS Basin, Badran, Kalibawang, and Blawong are the three most vulnerable irrigation sand traps, with sediment yield values of 252.83, 178.92, and 63.49 tons/ha/year, respectively; they are all located in sub-watershed outlets. The vulnerability assessment conducted in this study can be used for the decision support system to prioritize irrigation sand traps towards a more effective irrigation system development.