Lake sturgeon (Acipenser fulvescens) occupy the St. Clair River, part of a channel connecting lakes Huron and Erie in the Laurentian Great Lakes. In the North Channel of the St. Clair River, juvenile lake sturgeon (3–7 years old and 582–793 mm in length) were studied to determine movement patterns and habitat usage. Fourteen juveniles were implanted with ultrasonic transmitters and tracked June–August of 2004, 2005 and 2006. Telemetry data, Geographic Information System software, side-scan sonar, video images of the river bottom, scuba diving, and benthic substrate samples were used to determine the extent and composition of habitats they occupied. Juvenile lake sturgeon habitat selection was strongly related to water depth. No fish were found in <6 m of water and over 97% of the relocations were found at depths greater than 9 m. Available water depths exceeding 18 m only represented 3.5% of the available habitat, however 34.9% of the relocations were found at depths exceeding 18 m. Juvenile lake sturgeon did not use most areas in proportion to their availability. Sturgeon avoided clay ledges and shallow areas with silt or soft clay, which comprised approximately 39% of the benthic habitat in the North Channel. A total of 300 out of 351 documented locations were on sand and gravel habitat types mixed with clay. Lake sturgeon > 700 mm in length selected sand and gravel areas mixed with zebra mussels and areas dominated by zebra mussels, while fish < 700 mm used these habitat types in proportion to their availability.