Hakone has rich nature throughout the four seasons. This includes indigenous forests of Beech, Himeshara (Stewartia monadelpha), and Kousa Dogwood (Cornus kousa) near Mt. Kamiyama. Woodlands and mountains are adorned with spring buds and Mamezakura (Cerasus incisa (Thunb) Loisei), while Kousa dogwood is abundant in the summer and the mountains are covered in colorful autumn leaves.

Another aspect of Hakone’s diverse nature is seen in the number of plants and animals carrying “Hakone” within their names. One finds, for instance, Hakone salamander, Hakoneashinagakogane (Hopilia communis), Hakonehosohanakamikiri (Parastrangalis hosohana), Hakonekometsutsuji, Hakoneran(orchid) (Ephippianthus sawasanus), etc. A number of these species have alerted the curiosity of foreign researchers since the Edo period, Kaempfer and Tumber, for instance.

Hakone also provides the best environment for bird watching. From the months of spring to summer, there are Thrushes, Japanese bush warblers, Great spotted woodpeckers, Gray wagtails, Great tits. From autumn to winter, waterfowl such as Mallards, Wigeons, Tufted ducks, and Spot-billed ducks can be seen. There are many other types of wild birds to be observed.
In recent years, Lake Ashinoko has offered a habitat for Common mergansers in the summer.