The Willamette River Basin encompasses 31,000 square kilometers of western Oregon and consists of twelve major subbasins, each with hundreds of individual streams and unique hydrogeomorphic regimes and river corridor conditions. In conjunction with environmental DNA (eDNA) sample collection to support occupancy modeling of native freshwater mussels across the Willamette River Basin, bed-material substrate was sampled to better characterize streambed sediment grain sizes. Between August and December 2024, surficial particle counts were conducted at 105 sites ranging from small mountain streams to larger river corridors. Approximately 7-12 sites were sampled within each of the twelve major subbasins using gravelometers and a modified version of the Wolman sampling method (Wolman, 1954; Jones and Keith, 2021). Within each subbasin, sites were randomly selected based on site access and other factors with an overall objective of characterizing riverbed substrate and implications for potential mussel habitat. This data release summarizes particle count data collected at each of the 105 sample sites, providing grain-size distributions and summary statistics, including the 16th, 50th, and 84th percentile diameters (D16, D50, and D84, respectively) for sites where particle counts measurements were collected. This dataset includes several sites where particle count measurements were not collected but the associated site data is included for correlation with eDNA sampling data collected at those sites. Though these data were collected to support occupancy modeling of native freshwater mussels across the Willamette River Basin, this dataset is also useful for characterizing streambed sediment conditions and variability across the Willamette River Basin. Jones, K.L. and Keith, M.K., 2021, Surficial and subsurface grain-size data for the Siletz River, Oregon, 2017-18: U.S. Geological Survey Data Release, https://doi.org/10.5066/P96ZXPP. Wolman, M.G., 1954, A method of sampling coarse river-bed material: Transactions American Geophysical Union, v. 35, no. 6, p. 951-956.