The data set contains sampling and catch data associated with a broad-scale experiment to examine dispersal of endangered pallid sturgeon (Scaphirhynchus albus) free embryos 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 and recaptured through 20190708 from six sampling sites in a 150-mile reach of the Missouri River. The free embryos were sampled using multiple boats and crews at the sites, and sampling for the free embryos was conducted at the river bed (bottom samples), in the middle of the water column (mid-water samples), and at the river surface (top samples). The data set includes sampling location information, ichthyoplankton catches for the released pallid sturgeon free embryos and other Acipenseriformes species (shovelnose sturgeon Scaphirhynchus platorynchus, paddlefish Polyodon spathula), biological metrics for the Acipenseriformes free embryos, and genetic results used to identify Acipenseriformes species.