Wood Storks are designated an endangered species because of the declines in their population size. The endangered classification means that there is a concern that this species could become extinct if negative impacts continue. The Endangered Species Act under which the stork is protected states that it is unlawful to harass, harm, pursue, capture or collect this species anywhere within the U.S. The habitats that these birds need ("critical habitat") is also protected by law. There are also provisions in most states in which the species occurs that protect it under state law.

According to the Wood Stork Recovery Plan, the main cause of population decline has been loss of wetland foraging habitat, and adverse effects of water level manipulations on foraging and breeding. An intensive effort is now underway to restore populations of the stork to acceptable levels. The massive Everglades Restoration Plan is underway, and is aimed primarily at restoring the natural timing and flows of surface water, especially to the coastal areas of the Everglades where the storks used to nest. Impoundments at several locations in the southeast have been managed specifically to accomodate feeding and breeding by storks, notably at the Harris Neck National Wildlife Refuge, and the Kathwood Ponds (National Audubon Society) near Jackson, S.C.. Stork feeding habitat is also being enhanced at many other national wildlife refuges, in rice-field impoundments and other publicly owned land.

Will storks ever recover to their former population sizes? The revised Wood Stork Recovery Plan recommends that the species be considered for upgrading from federally Endangered to Threatened status if the southeastern U.S. population increases to 6,000 nesting pairs (3-year average), and annual regional productivity of >1.5 chicks per nest per year. For removal of all federal protection status under the Endangered Species Act, the storks would need to increase to over 10,000 nesting pairs (5-year average, 50% of historical population), >1.5 chicks/nest, and a minimum of 2,500 successful nesting pairs in south Florida. There are some signs of increasing trends in recent years, including increases in the proportion of years in which storks nest successfully in the Everglades, and mild increases in nesting population of the southeastern population (see population and the Wood Stork Newsletter).