The Eagle Cap Wilderness is characterized by high alpine lakes and meadows, bare granite peaks and ridges, and U-shaped glacial valleys. Thick timber is found in the lower valleys and scattered alpine timber on the upper slopes. Elevations in the wilderness range from approximately in lower valleys to at the summit of Sacajawea Peak with 30 other summits exceeding . The wilderness is home to Legore Lake, the highest lake above sea level in Oregon at , as well as more than 60 named alpine lakes and tarns (12 of which are above 8,000 feet), and more than of streams.