Yukon Delta NWR contains approximately 22 million acres within the northern boreal zone of southwestern Alaska. About 70% of the refuge is below 100 feet in elevation and consists of a broad, flat delta dotted with countless waterbodies. The delta was created by the Yukon and Kuskokwim rivers and their tributaries. The Yukon River delta is in the process of building up, while the Kuskokwim delta is slowly being eroded by normal river processes. Many streams and sloughs are former tributaries of the two major rivers. Flooding of riverine and lowland areas is common, particularly in spring. The refuge's extensive tidal wetlands are scarcely above sea level and are frequently inundated by Bering Sea tides.
The coastal plain is contrasted by uplands and mountains to the north, east, and south. Several small mountain groups are scattered across the coastal plain. The southern extension of the Nulato Hills is located near the refuge's northern boundary. These rounded hills, rising from 1,000 to 3,000 feet in elevation, are the western extension of this large geographic feature. The Askinuk Mountains are located along the refuge's western coast, immediately south of Scammon Bay. They are approximately 10 by 32 miles in size and are the only part of the coastal plain that has been glaciated. The Kusilvak Mountains are located approximately 40 miles west of the village of St. Mary's and are directly south and east of Nunavaknuk Lake. They are eight miles from north to south, and five miles east to west, rising 2,200 feet. The Ingakslugwat Hills north of Baird Inlet are a group of small volcanic cones, lava flows, and craters. The tallest of these is 650 feet. These hills may be one of the most recently active volcanic areas on the Delta. The Kilbuck Mountains are a western extension of the Kuskokwim Mountains and are located in the southeast part of the refuge. These mountains range from 2,000 to 4,000 feet in elevation.
Two major islands are located within the refuge. The million-plus acre Nunivak Island lies 20 miles off the coast and is of volcanic origin, with several peaks from 1,000 to 1,600 feet. Coastal bluffs range from 100 to 450 feet high. Sandy beaches along the southern coast merge into active sand dunes greater than 100 feet in height. These dunes are particularly susceptible to erosion because protective foredunes and extensive beaches are absent. The second largest island is Nelson Island, which is separated from the mainland by the Ninglick River to the north, Baird Inlet to the northeast, and the Kolavinarak River to the east. The southern portion of the island is low-lying and covered with small lakes and streams. To the north, the terrain becomes more rugged with several peaks of over 1,300 feet in elevation.
Refuge vegetation is primarily subarctic tundra, underlain by permafrost, and includes a variety of scrub, peatland, heath meadow, marsh, and bog habitats. Tall scrub and forest habitats are found not just in the eastern interior, but along both major riers. On the Yukon, these habitats reach nearly to the Bering Sea. Alpine tundra occurs in the mountainous areas at higher elevations. Virtually no habitat management, as is commonly practiced on refuges in the lower 48 states, occurs on the refuge. Habitat related activities involve mapping and inventory efforts associated with specific wildlife studies and wildlife management.
The two largest rivers in Alaska, the Yukon and the Kuskokwim, flow across the refuge and are the primary architects of the refuge’s landscape. Most of the refuge is a vast, flat wetland/tundra complex dotted by countless ponds, lakes, and meandering rivers. In fact, approximately half of the refuge is covered by water. The refuge's most productive wildlife habitat is the coastal region bordering the Bering Sea between Nelson Island and the Askinuk Mountains. This narrow strip of wetland habitat is unquestionably the most productive goose and shorebird nesting habitat in Alaska. For the most part, aquatic habitat on the refuge is considered to be relatively unaltered by people, but past and present mining activities have simplified stream habitat in several areas adjacent to the refuge boundary (e.g., Tuluksak River), and may have reduced the productivity of those streams.
Less than five percent of the refuge is forested. Narrow bands of riparian, black spruce-hardwood, mixed black spruce-balsam poplar,
and balsam poplar woodlands extend onto the delta along the Yukon and Kuskokwim Rivers and their tributaries. In addition, pockets of black spruce and white spruce are interspersed throughout the Kilbuck Mountains and Andreafsky River watershed. A recent economic analysis suggest otherwise.