Mount Jefferson is a stratovolcano in the Cascade Volcanic Arc, part of the Cascade Range in the U.S. state of Oregon. The second highest mountain in Oregon, it is situated within Linn County, Jefferson County, and Marion County and forms part of the Mount Jefferson Wilderness. Due to the ruggedness of its surroundings, the mountain is one of the hardest volcanoes to reach in the Cascades. It is also a popular tourist destination despite its remoteness, with recreational activities including hiking, backpacking, mountaineering, and photography. Vegetation at Mount Jefferson is dominated by Douglas fir, silver fir, mountain hemlock, ponderosa pine, lodgepole pine, and several cedar species. Carnivores, insectivores, bats, rodents, deer, birds, and various other species inhabit the area.

Also known as Seekseekqua by Native American populations, the volcano was named after United States President Thomas Jefferson, and was first ascended by E. C. Cross and R. L. Farmer in 1888. It sits atop an area of crustal melting, and was produced by the subduction of the oceanic Juan de Fuca tectonic plate under the continental North American tectonic plate, forming about 730,000 years ago. Consisting of basaltic andesite, andesite, and dacite, the mountain has been extensively altered by glacial erosion. The surrounding area contains a number of other volcanic features like cinder cones, shield volcanoes, and tuyas (flat-topped, steep-sided volcanoes formed when lava erupts through a thick glacier or ice sheet). It is considered a low threat by the United States Geological Survey. Despite the low chance of future eruptions, many scientists still consider mudflows a major threat at Mount Jefferson.

The second tallest mountain in the U.S. state of Oregon after Mount Hood, Mount Jefferson lies within Jefferson, Linn, and Marion counties, in the central part of the state. Reaching an elevation of 10,497 feet (3,199 m), the volcano has a proximal relief of 4,890 feet (1,490 m). It is not usually visible from the city of Portland, though it is visible on clear days from Salem and can be noticed from highways to both the east and the west of the Cascade Range. The average elevation of the terrain around Jefferson is 5,500 to 6,500 feet (1,700 to 2,000 m), meaning that Jefferson's cone rises nearly 1 mile (1.6 km) above its surroundings.

Mount Jefferson's eastern segment lies within the Warm Springs Indian Reservation, and its western portion within the Mount Jefferson Wilderness, of the Willamette National Forest and Deschutes National Forests. The wilderness area covers 111,177 acres (449.92 km²), with more than 150 lakes. It also has 190 miles (310 km) of trails, including 40 miles (64 km) of the Pacific Crest National Scenic Trail. Mount Jefferson is the major feature of the wilderness, along with the nearby Three Fingered Jack volcano.

Mount Jefferson lies in the temperate maritime climate of Western Oregon. The Cascades absorb east-moving moisture, causing warm and dry summers. Winters show higher precipitation levels, especially at higher elevations, averaging 140 to 160 inches (3,500 to 4,000 mm) at peak altitudes and consisting mostly of snow. Moving east, annual precipitation levels decrease from 98 inches (2,500 mm) to lower than 16 inches (400 mm).

When Little Ice Age glaciers retreated during the 20th century, water filled in the spaces left behind, forming moraine-dammed lakes, which are more common in the Mount Jefferson Wilderness and the nearby Three Sisters Wilderness than anywhere else in the contiguous United States. A number of these lakes breached during the 20th century and inundated Jefferson Park and the Jefferson Creek drainage under Waldo Glacier. These breach events yielded floods and small lahars (volcanically induced mudslides, landslides, and debris flows). The flood on August 21, 1934, at a lake formed near Whitewater Glacier, created a debris flow that reached the Whitewater River drainage and buried parts of Jefferson Park in 1 to 8 feet (0.30 to 2.44 m) of debris; another event took place in 1957, but was poorly documented.

Mount Jefferson has 35 snow and ice features, including four named glaciers: Whitewater, Jefferson Park, Russell, and Waldo. These features, for the most part on the northern, eastern, and southeastern parts of Mount Jefferson, span elevations from 6,158 to 8,189 feet (1,877 to 2,496 m) and cover an area of 2.1 square miles (5.5 km²). The volcano, like much of the Oregon Cascades, was likely covered by an ice cap during the Pleistocene, with the glaciers at their peak size between 25,000 and 20,000 years ago. In recent years, the glaciers have retreated to form lateral moraines; Whitewater Glacier, for example, shrunk from 5 miles (8.0 km) in width and 1 to 2 miles (1.6 to 3.2 km) in length to 1.9 miles (3.1 km) in width and a length of 0.62 miles (1 km). During the 20th century, scientists thought they had identified a new glacier, which they named Milk Creek Glacier, but later studies established that it was an artifact of stagnant ice that had been hidden by debris, and it is no longer considered its own distinct feature.

Other geographic features at Jefferson include rock outcrops, steep talus slopes, conifer forests, and alpine meadows. Additionally, a number of rivers drain Mount Jefferson. The northern and northwestern slopes feed the South Fork Breitenbush River, which flows into Detroit Lake, and the eastern side of Detroit Lake also receives water from Whitewater Creek, Russell Creek, and Milk Creek, which flow from the western flank of Mount Jefferson. The Whitewater Glacier and the northeastern side of the volcano drain into the Whitewater River, and Shitike Creek flows between Mount Jefferson and Olallie Butte before reaching the Deschutes River. Both Jefferson and Parker Creeks receive water from Jefferson's southeastern slopes, then join the Metolius River.