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.

The coastline enclosing the lagoon supports a range of vegetation types dominated by heathlands of Acacia leiophylla and Orthrosanthus multiflorus, herb lands of Senecio odoratus, coastal mallee scrub of Eucalyptus diversifolia, samphire flats and grazed grasslands.

These include sand crab, king scallop, queen scallop, razorfish (Pinna bicolor), southern calamari, flathead, King George whiting, leatherjacket, red mullet, snook, Southern Sea garfish, tommy ruff, trevally and Western Australian salmon.

[13] As early as May 1905, fishing by the use of nets was prohibited both in Pelican Lagoon and adjoining waters in both American River and Eastern Cove.

[14] As early as 1908, the role of ‘Pelican Lagoon on the American River’ as a hatchery area was acknowledged by the South Australian government via statements attributed to Mr. S. McIntosh, the then Deputy Chief Inspector of Fisheries.

[16] The islands within the lagoon first obtained protected area status as a fauna conservation reserve declared under the Crown Lands Act 1929-1966 on 16 March 1967.