Leque Island is located at the mouth of the Stillaguamish River on the South Pass channel, which separates Camano Island from the mainland, approximately 43 miles (69 km) north of Seattle and 0.6 miles (1 km) southwest of Stanwood, Washington. The island is named after Nels P. Leque, who settled there in 1876 when it was a tidal salt marsh. The marsh was bisected by a slough used by Native Americans in canoes as a shortcut between Davis Slough and West Pass. The underlying bedrock dates back to the Miocene era and is covered by 1,000 to 3,100 feet (305 to 945 m) of glacial and non-glacial sediment. The nutrient-rich soil on Leque Island was deposited as a lahar, a violent type of mudflow, which flowed down the river valley from a Glacier Peak eruption approximately 12,500 years ago. The salt marsh deposits mainly consist of silt and clay, often interspersed with lenses and layers of peat and other organic material originally deposited in saltwater or a brackish marsh environment. Many of these deposits have been converted to agricultural use through the construction of levees. Repeated flooding by the Stillaguamish River continues to deposit nutrients and sediment.

Archaeological evidence suggests humans began living here around 6,000 years ago. The Coast Salish tribes inhabited the Skagit River delta and were closely associated with the Upper Skagit River tribes. The Stillaguamish people camped on nearby Camano Island. In 1792, Captain George Vancouver and Lieutenant Joseph Whidbey observed villages there while exploring Puget Sound. By the mid-1800s, adventurous Euro-Americans reached the Washington Territory, and entrepreneurial lumbermen discovered the tall Douglas fir trees on Camano Island. These trees were initially cut for ship spars and wharf pilings, then loaded onto sailing ships for transport to San Francisco or foreign ports. In 1856, a sawmill was constructed in Utsalady Bay on Camano Island. At that time, Leque Island was a tidal area with about 400 acres (162 ha) of salt marsh and 100 acres (40 ha) covered with logs and debris. In the early 1870s, Jerome N. Barry and his brother established a logging camp at the south end of Leque Island. In 1876, Norwegian immigrant Oliver B. Iverson partnered with Nils Eide, Nels P. Leque, and Andy Danielson to begin farming on the island. They diked and drained the land to grow oats and hay and pastured cattle. These families farmed Leque Island for several generations before eventually selling the parcels to other farmers. Since 1974, the Washington State Department of Fish and Wildlife has acquired 325 acres (132 ha) of the island, contracting farmers to plant grains for wintering waterfowl. Recently, repeated dike failures have prompted restoration efforts.

In 2007, the Port Susan Marine Stewardship Area was established, encompassing the entire Port Susan Bay, including the shoreline and Leque Island. This stewardship is managed by various environmental groups working to improve the health of the local waters. Changes to the estuaries and marshes on Leque Island, such as diking and draining for agricultural purposes, have been identified as threats to the marine ecosystem. In response, the Washington Department of Fish and Wildlife began acquiring properties on Leque Island in 1974 and now owns the entire island. The Leque Island Estuary Restoration Project was undertaken by Ducks Unlimited, the Stillaguamish Tribe, The Nature Conservancy, and Skagit River System Cooperative. In 2019, the project removed over 2.4 miles (3.8 km) of levee and restored 250 acres (101 ha) of tidal marsh, creating vital habitat for juvenile Chinook salmon and shorebirds. Since the removal of the dike, 15 different species have been observed utilizing the restored area, including juvenile Chinook, chum, and coho salmon, and adult bull trout. Read more here and here. Explore more of Leque Island and South Pass Stillaguamish River here: