West coast redwood trees dominate Muir Woods' forest. Douglas-fir, big-leaf maple, tanbark oak, and baylaurel grow along side the redwoods. At the lower end of the canyon, red alders line the stream and buckeyes cluster nearby. Baylaurels growing toward the light may assume contorted shapes or topple over.

Each season at Muir Woods has its own character. Fall is warmest: ladybugs swarm, crayfish are active in Redwood Creek, and the leaves of big-leaf maple turn yellow and drop. During winter, steelhead (migratory rainbow trout) and silver salmon migrate up Redwood Creek to spawn, and toyon berries turn a vibrant red. In spring, birds nest, wildflowers dot Redwood Canyon, and blacktail deer birth spotted fawns. Summer is the season of fog, azaleas, aralias, buckeyes, Steller's jays, and chipmunks.