In 2019, an experimental release of nearly 1.0 million free embryos of federally endangered pallid sturgeon (Scaphirhynchus albus) was conducted in the Missouri River of eastern Montana and western North Dakota. Dispersal of the free embryos and survival of the benthic larvae was assessed from 20190701 to 20190909 through 150 miles of the river. The data sets contain mean daily discharge and hourly water temperature data for the Missouri River, and mean daily discharge data for the Yellowstone River. Dates of the data extend from 20190701 to 20190909. Discharge data for the Missouri River were obtained from USGS gage 06177000 near Wolf Point, Montana. Discharge data for the Yellowstone River were obtained from USGS gage 06329500 near Sidney, Montana. Water temperature data for the Missouri River were recorded by water temperature loggers positioned near Poplar, Montana, Culbertson, Montana, the Montana-North Dakota state border, and downstream from the Yellowstone River confluence.