We conducted the first continuous shipboard tracking of southern Distinct Population Segment green sturgeon, Acipenser medirostris, in the Sacramento River. Tracking of adult green sturgeon occurred between river kilometer (rkm) 434.8 and 511.6, a section of the putative spawning grounds located near Red Bluff, California. The recorded positions of acoustically tagged green sturgeon were analyzed using First Passage Time analysis to determine differences in habitat use between suitable and non-suitable habitats. Classification and Regression Tree modeling was used to determine explanatory inputs attributable to above average habitat use. Green sturgeon exhibited above average habitat use at five sites, identified as potential spawning aggregate sites. Three types of movements (holding, milling, and directed) could be categorized from tracks. Lastly, we show that green sturgeon while on the spawning grounds exhibit a high degree of mobility throughout the spawning grounds, often making large movements between specific habitat units. Our study illustrates how the application of shipboard tracking can be useful for describing movement, behavior and habitat utilization at a spatial scale not achieved by stationary acoustic monitors.