Tokyo is well known for being one of the largest and most populated cities in the world. While its neon-lit skyline and bustling city life attracts one of the highest volumes of tourists in Japan, many tend to feel in need of a little getaway after travelling around Tokyo for a while. If you’re the type of person that loves nature, these are the places that you should consider including in your itinerary as a side trip from Tokyo.
Kamakura

Kamakura is a coastal town in Kanagawa Prefecture, famed for its rich heritage. Sometimes called the Kyoto of Eastern Japan, Kamakura is covered in temples, shrines and other historical monuments that are surrounded by lush forested areas.

One of the most iconic attractions of Kamakura is the Great Buddha Statue, the 2nd largest bronze statue in Japan. Other attractions include Hasedera, Hokokuji and Kenkoji temples, and Hachimangu Shrine.

Kamakura has numerous hiking trails for those looking to immerse themselves in nature. There are also several sandy beaches which are very popular during the summer months, and can get a bit crowded.
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Kamakura is located less than an hour south of Tokyo, and is easily accessible by train. Some opt for the Enoshima Kamakura Free Pass, which includes a round trip and is great if paired with a trip to Enoshima (more on this later), otherwise it can be reached in 1 hour for about 1000 yen.
Nikko

Nikko is a gorgeous city that houses the main areas of Nikko National Park, in Tochigi Prefecture. Known as one of the most beautiful national parks in Japan, Nikko National Park is famed for its mountainous landscapes, waterfalls, hot springs and hiking trails.

Nikko had been a centre of ancient Shinto and Buddhist worship for many centuries. Most notably, Futarasan Shrine, Tōshō-gū shrine and Rinnō-ji temple are designated UNESCO world heritage sites, with Tōshō-gū being a particular highlight.

The Shinkyo Bridge is a symbol of Nikko, and Kanmangafuchi Abyss, a beautiful gorge, can be enjoyed from a riverside walking trail. Lake Chuzenji is also one of Nikko’s main draws.
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There are several travel passes (click here) which include round trips from Tokyo, and are valid from 2-4 consecutive days. The best option for a day trip is the Nikko City area pass, which is valid for 2 days and is considerably cheaper than individual train tickets at only 2670 yen.
You can consider purchasing the JR Tokyo Wide Pass, which is valid for 3 days, for 10,000 yen if you plan to take more day trips to other areas, otherwise the Nikko city area pass is enough.
Hakone

Hakone is a beautiful town in Kanagawa prefecture, that is part of the Fuji-Hakone-Izu National Park. Famous for its numerous hot springs, Ryokans and the view of Mount Fuji across Lake Ashinoko, Hakone is one of the most popular destinations among both Japanese and international tourists looking for a break from the concrete jungle that is Tokyo.

Well known attractions of Hakone include Owakudani- the active volcanic zone, the Open Air Musuem, Hakone Shrine, and of course, Lake Ashinoko. Owakudani is where you can try the true onsen eggs, which are boiled in sulfuric waters.

The Hakone Ropeway (covered by the Hakone free pass!) is a popular way to visit Hakone, as it stops at Owakudani and Ubako stations on the way to Togendai Station (at the shore of Lake Ashinoko).
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Located less than 100 kilometers away, Hakone is easily accessible by both train and coach. Many opt for either the Fuji Shizuoka Tourist Pass (8,000 Yen, 3 days) or the Hakone free pass (5,140 yen, 2 days), both of which have round trip options. Others opt to take the Romance car, which is more expensive (additional 890 yen).
Kusatsu

Kusatsu is a town in Gunma prefecture, and is one of Japan’s most famous hot spring resorts. The town boasts large volumes of high-quality hot spring water in natural onsens, some of which can be found within lovely traditional ryokans.

Some of the most popular open-air baths include Sainokawara Rotenburo onsen – an open-air bathhouse with beautiful views, Otakinoyu onsen- a bathhouse with traditional wooden interiors and outdoor options, and Gozanoyu – a bathhouse with a stone and wooden bath.

Being a mountainous town, Kusatsu also offers skiing in winter and hiking during the rest of the year, with the most famous ski resort being the Kusatsu Ski Resort. The active volcano Mt. Shirane, also known as Kusatsu-Shirane is also a popular spot to visit.
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This trip is ideal for those with JR passes, as train is required to reach Naganohara-Kusatsuguchi Station (2 hours by limited express) before taking a JR bus to Kusatsu (30 minutes). This train trip is otherwise very expensive. You can consider purchasing the JR Tokyo Wide Pass, which is valid for 3 days, for 10,000 yen, which is already cheaper than 1 round trip.
If you do not have a JR pass, taking the JR highway buses from Tokyo (Shinjuku JR Highway Bus Terminal) is the cheapest and most convenient option. The one way trip costs 3300 yen and takes about four hours, and hence is more suitable for those with an extra day to spare.
Enoshima

Only a short train ride from Kamakura, Enoshima is a wonderful but slightly touristy island in Kanagawa Prefecture. This popular retreat has some of the nearest beaches from Tokyo. Views of Mount Fuji can be enjoyed on days with good visibility.

The forested hill of Enoshima contains most of its attractions. Enoshima Shrine, consisting of several structures are found around the island. The island’s beaches and caves are also very popular during summer.

At the end of a short walking trail sits a love bell, which is said to strengthen the relationship of couples who ring it together. At top of Enoshima’s hill, the bell overlooks a nice view of the ocean. The southern coast also features cliffs.
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Enoshima can be explored as its own day trip, but many choose to visit it together with Kamakura due to its proximity. Buying the Enoshima Kamakura Free Pass, which includes a round trip, is ideal only for the latter case. Buying local train tickets is ideal if you only want to go to Enoshima as it only costs 630 yen.
If only going to Enoshima, buying the Enopass for free admission (garden, observation tower, caves) and discounted admission to the island’s attactions is recommended.
Yuzawa

Yuzawa is a resort town in Niigata Prefecture is one of the largest and the most easily accessed ski areas from Tokyo. The Japanese Alps of Yuzawa offer high quality, powdery snow for an abnormally long season, with some of its resorts open from mid-November to late May.

There are approximately twenty resorts around Yuzawa, varying from one to thirty lifts, the most famous being Gala Yuzawa Resort. The town is also known for their onsens, which are popular after a day full of winter sports.

Apart from its famous winter beauty, Yuzawa’s mountains also shine in other seasons, showcasing untouched natural scenery that tourists seem to overlook (as it is heavily branded as a winter destination). The gondola is a great way to view the foliage.
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Echigo-Yuzawa Station can be reached from Tokyo Station in 80-90 minutes by the Joetsu Shinkansen. This trip is ideal for those with JR passes as it is otherwise very expensive. You can alternatively purchase the JR Tokyo Wide Pass, which is valid for 3 days, for 10,000 yen that will take you further to Gala Yuzawa station instead (winter & spring) and is already cheaper than a round trip.
Lake Kawaguchiko (Mt. Fuji)

Lake Kawaguchiko is one of the 5 lakes that surrounds the World Heritage site and symbol of Japan, Mt. Fuji. Among the 5 lakes it is considered a particular stand out, providing many excellent viewpoints for gazing at the mountain.

Attractions available around Lake Kawaguchiko include various onsens, museums, the very popular Fuji Q amusement park, boat tours around the lake and a ropeway. If time permits you can explore some of the other 4 nearby lakes.

The Kachi Kachi Ropeway ascends to an observation point near the summit of Mount Tenjo, from where Lake Kawaguchiko and Mount Fuji can be seen. The area is particularly beautiful in Spring, when shibazakura are in full bloom at the nearby Fuji Motosuko Resort.
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Local Buses, known as retro buses, can be taken to reach Lake Kawaguchiko from Kawaguchiko Station (nearest station). You can easily reach Kawaguchiko station through the JR Chuo line in 2 hours, and only costs 2460 yen or through the even cheaper highway bus from Shinjuku Expressway Bus Terminal.

[adapted from my now missing odigo page]