We observed extensive mortality (eggs and chicks) of the endangered interior population of the Least Tern (Sterna antillarum) and threatened Piping Plover (Charadrius melodus) caused by natural flooding during the 1990 breeding season along the Platte River, Nebraska USA. Aerial videography of the Platte River before and after the flood revealed a 78% reduction of perennial vegetation on sandbars. The flood scoured vegetation from sandbars and greatly increased the amount of barren sandbar habitat that nesting Least Terns and Piping Plovers use. A review of river gauging station data indicated that flooding of the 1990 magnitude or greater can be expected to occur about once every nine years. We recommend a review of the annual operating plans of managed rivers to account for the effects of dam discharges on Least Terns and Piping Plovers.