Stream classifications are important for understanding stream ecosystem diversity while also serving as tools for aquatic conservation and management. With current rates of land and riverscape modification within the United States (US), a comprehensive inventory and evaluation of naturally occurring stream habitats is needed, as this provides a physical template upon which stream biodiversity is organized and maintained. To adequately represent the heterogeneity of stream ecosystems, such a classification needs to be spatially extensive where multiple stream habitat components are represented at the highest resolution possible. Herein, we present a multi-layered empirically-driven stream classification system for the conterminous US, constructed from over 2.6 million stream reaches within the NHDPlus V2 stream network. The classification is based on emergent natural variation in six habitat layers meaningful at the stream-reach resolution: size, gradient, hydrology, temperature, network bifurcation, and valley confinement. To support flexibility of use, we provide multiple alternative approaches to developing classes and report uncertainty in classes assigned to stream reaches. The stream classification and underlying data provide valuable resources for stream conservation and research.