While much literature exists on the ecology and ecosystem impacts of signal crayfish, Pacifastacus leniusculus (Dana, 1852), as an invasive species, little information exists on the ecology of this species in its native range in the Pacific Northwest, USA. Signal crayfish (P. leniusculus leniusculus) were collected from the Umatilla River in northeastern Oregon, USA, where they are native. Collecting occurred during the summer at 13 sites spanning the longitudinal gradient of the river to examine the relationship between density and size of individuals and environmental factors at two spatial scales. At the reach scale (100 m²) the density of young-of-year (YOY), and age 1 female and male crayfish was positively associated with substrate size. Additionally, age 1 female and male crayfish density was negatively associated with the amount of crop agriculture. Substrate size was also important in determining the density and size of crayfish at the microhabitat scale (<1 m²) with greater densities and larger size (for age 1 females and males) with larger substrate. Other factors influencing density at the microhabitat scale included Froude number for YOY and age 1 females with higher densities at lower Froude numbers (indicative of tranquil flows) and water depth for age 1 males with higher densities at greater depth. Our results indicate that substrate size is one of the most important drivers of the distribution and density of signal crayfish in the Umatilla Basin at multiple spatial scales. Understanding the habitat requirements and ecology of this species in its native range is important as agricultural intensification resulting from the development of biofuel technology and increasing human population size and the threat of invasive crayfish species might greatly influence the distribution, abundance, and management of the species of Pacifastacus in their native range in the near future.