Pelican Lagoon is a seawater lagoon in the Australian state of South Australia located on the north coast of Kangaroo Island about 18.7 kilometres south east of Kingscote. It was named by Matthew Flinders on 4 April 1802 after the large population of pelicans present in its waters and adjoining shorelines. Its role as fishery hatchery had been identified by the early 20th century with the result that fishing in its waters has been restricted in varying degrees.
Since 1971, the entire lagoon was part of a marine protected area known as the American River Aquatic Reserve (abolished 2016), where all fishing and the collection of marine organisms is prohibited. Since 2012, the Pelican Lagoon Sanctuary Zone has been within Encounter Marine Park and managed by National Parks South Australia. The lagoon is probably the oldest marine protected area in South Australia, having been protected since 1914.