The data set contains sampling data, catch data, and biological data associated with a broad-scale experiment to examine free embryo dispersal and larval settlement of endangered pallid sturgeon (Scaphirhynchus albus) in the Missouri River of eastern Montana and western North Dakota. On 20190701, two age groups of pallid sturgeon including 771,707 1-day post-hatch (dph) free embryos and 200,786 5-dph free embryos were released in the Missouri River where dispersal in the water column was assessed through 150 miles. Following dispersal, beam trawl sampling of benthic habitats was conducted to verify settlement and quantify the spatial extent of settlement. Trawling was conducted for nine consecutive weeks from 20190716 to 20190911 in eight river bends positioned between river miles 1552.0 and 1591.8. A tissue sample was obtained from captured larval Scaphirhynchus. The tissue sample was used in genetic analysis to identify species and identify parentage. The data set includes sampling location information, benthic trawl catch data for Scaphirhynchus species and other species, genetic results distinguishing Scaphirhynchus species as shovelnose sturgeon or pallid sturgeon, parentage for the pallid sturgeon, and biological data for all species.