A large lahar from a Glacier Peak eruption 12,500 years ago created the island and brought most of the alluvial soils.

Early written accounts describe the island as a place of portage to the Olympic Peninsula, and tell of a local leader known as "Split-Lip Jim" who rented canoes and women to row them.

Since 1974, the Washington Department of Fish and Wildlife has purchased 325 acres (132 hectares) of the island and contracted farmers to plant grains for wintering waterfowl.

More recently, Leque Island had suffered repeated levee failures, which endangered the local roadway, Washington State Route 532.

The groundwater of the island, flowing from east to south, is usually found one foot or less from the surface, with the result that exposed seeps discharge into the man-made drainage ditches.

[2] The uncultivated parts of the island are mainly covered in an invasive non-native species, such as reed canary grass, holly, Himalayan blackberries, tansy, St Johns wort, oxeye daisies and stinky Bob.

Other native plants on the island include yarrow, lady and sword ferns, blue aster, thistles, sweet pea, clovers, rose hips, fireweed, plantain, a stand of dead cottonwoods Populus sect.

The wildlife on the island itself consists mostly of a large and diverse bird community, including marsh hawks, western sandpipers, loons, seagulls, peregrine falcons, ducks, geese, great blue herons, golden eagles, pheasants (stocked), dunlins, phoebes, least sandpipers, greater yellowlegs (Tringa melanoleuca), black-bellied plovers (Pluvialis squatarola).

Marine organisms in the surrounding water, which have been identified by the Port Susan Marine Stewardship Conservation Action Plan, are: A study by the Stillaguamish Tribe's Natural Resources Department, in conjunction with Pacific Coastal Salmon Recovery Funding, about Stillaguamish Estuary Use by Juvenile Chinook, established that the Port Susan area, which envelopes Leque Island and extends southward, hosts two genetically distinct populations of Chinook salmon.

[7] The study showed that threatened Chinook around Leque Island depend on its estuaries, and recommended the restoration of these habitats to their wild state.

The changes in the estuaries and marshes on Leque Island, carried out to promote agriculture, such as diking and draining, were identified as one of the threats to the marine ecosystem in the area.

About 100 acres (40 hectares) would be conserved for the established freshwater wetlands and mixed recreational use, including increased access for those with limited mobility, and some agriculture.

[8] The Salmon Recovery Funding Board identified these changes as important for improving rearing habitat for juvenile salmonids, including at least two threatened species.