AbstractSediment transport modeling (STM) is a potentially effective tool for estimating the magnitude of tsunamis and earthquakes without historical records. However, the application of STM to prehistorical tsunamis is challenging because of multiple uncertainties in topography and roughness. Along the coast of Hidaka, Hokkaido, Japan, there is potential to conduct STM even in the absence of historical records because comprehensive geological data for the coastal evolution during the Holocene are available here. The tsunami deposits in Hokkaido indicate the presence of events on a larger scale than historical tsunamis; in particular, the seventeenth‐century tsunami had multiple potential wave sources other than a Kuril Trench earthquake, inhibiting its magnitude estimation. In this study, we applied STM to paleotsunamis for the coast of Hidaka, where comprehensive geological data are available, although the wave source is unknown. The modeling parameters—paleotopography, roughness, grain size, initial sand source, sea level, and beach ridge height—were estimated using data obtained from geological surveys and sensitivity tests. The modeling of a tsunami induced by a Kuril Trench earthquake reproduced the sediment distributions and sedimentary structures of the observed sand layers better than that of extreme storms and volcanic tsunamis. Because the conventional fault model is reasonably suitable in the western area from the Kuril Trench, a much wider rupture zone is less likely. Parameters such as sand source area, roughness, ridge height, and paleo sea level are important for geologists and modelers when applying STM to paleotsunamis.