Yosemite is one of the largest and least fragmented habitat blocks in the Sierra Nevada, and the park supports a diversity of plants and animals. The park has an elevation range from 2,000 to 13,114 feet (600 to 4,000 m) and contains five major vegetation zones: chaparral/oak woodland, lower montane, upper montane, subalpine, and alpine.

The bedrock of the Yosemite region consists of granite and granodiorite plutons, part of the Sierra Nevada batholith, which formed deep in the crust as intruding magma during the Mesozoic Era. Subsequent uplift and erosion has re-exposed the plutons to the surface. The release of all that overburden pressure resulted in the formation of joints, concentric shell cracks referred to as exfoliation, in the rock that often result in the domes seen at many high peaks in the valley, including Half Dome. More recently, Pleistocene-age glaciers covered most of the area and scoured the valleys, creating the steep valley walls and hanging valleys where spectacular waterfalls now freefall.