The management of the Drowned Land of Saeftinghe is mainly concentrated on the preservation and development of its natural values. Next to that, many measures are taken to enable sustainable, nature oriented recreation. In general, this means optimising grazing management, protecting areas against disturbance and clear zones for recreational access. For certain species, such as common tern, spoonbill and Kentish plover, special measures are taken to improve breeding habitat.

The Dutch-owned part of Saeftinghe (3554ha) is currently managed by Stichting Het Zeeuwse Landschap, while the Flemish part is managed by 2 nature organisations: Agentschap voor Natuur en Bos (sub-site: Paardenschor, 14 ha) and Natuurpunt (sub-site: Schorren van Oude Doel, 51 ha).