Interactions between geomorphic processes at multiple scales shape the distributions of habitats, species, and life stages that a river can support. Understanding these hierarchical processes may be helpful for proactive monitoring and restoration of native Western Brook Lamprey (Lampetra richardsoni) and Pacific Lamprey (Entosphenus tridentatus) in Pacific Northwest rivers. The processes creating thick, fine-grained sediment deposits that lamprey larvae rely on as rearing habitat were assessed in part through field sampling in the Umpqua River basin, southwestern Oregon, USA. Local factors, such as substrate, boulders, wood, and water, that control sediment erosion and deposition, affecting larval lamprey habitat, were systematically mapped with a total station at the reach-scale for two reaches along Little Wolf, Slide, and South Fork Calapooya Creeks in the Umpqua River Basin, southwest Oregon. This overall dataset includes: 1) GIS layers defining the extent and grain-size of substrate patches, extent of the wetted water surface, locations of boulders, and locations of large wood for all six study reaches that are included in a file geodatabase, 2) a csv file of the raw particle counts used to determine the grain size of the sediment patches, and 3) a csv file of the lengths of larval lamprey detected in the reaches. The datasets were developed by completing geomorphic and larval lamprey surveys in 2014. This documentation describes the grain-size data for the upstream and downstream reaches of Little Wolf, Slide, and South Fork Calapooya Creeks from particle counts completed in July and August 2014.