This data set describes developmental and physiological effects observed in fathead minnow embryos that were exposed to sodium nitrate or conductivity-matched controls. Exposures were conducted in the laboratory from fertilization through 21 days post-fertilization (dpf). Nitrate doses were 0, 2, 5, 10, 25, or 100 milligrams per liter nitrate-nitrogen; conductivity controls were matched to the 10 and 100 milligrams per liter nitrate-nitrogen treatments. During the experiment, we assessed heart rate and percent arrhythmic heart beats at 3 dpf, timing of hatch and inflation of the posterior and anterior swim bladders, presence of pericardial edema or scoliosis, fish metrics at 21 dpf (fish length and weight; swim bladder length, width, and volume), and mortality. Water quality data during the exposure period are also presented, and include conductivity, pH, nitrate-nitrogen, total ammonia, unionized ammonia, and dissolved oxygen.