The predecessor of this national park, Matsalu Nature Reserve, was established in 1957 to protect birds and their nesting, moulting and stopover sites.
In 1976, Matsalu was added to the List of Wetlands of International Importance, or the Ramsar List. The Ramsar Convention recognises nature reserves where wetlands are preserved and used sustainably.
In 2004, the reserve was given the status of a national park. Besides birds, Matsalu National Park aims to protect landscapes characteristic of Western Estonia and the cultural heritage of the Väinameri Sea region.
Matsalu National Park has been awarded with European Diploma of Protected Areas by the Council of Europe in recognition of its efforts to protect biological, geological and landscape diversity in the area and in 2015 with European Charter for Sustainable Tourism in Protected Areas, which is issued by EUROPARC Federation.