For many travelers, it is a relief to know you can drink water from the tap throughout Japan without ill effects. You can rest assured that you will not catch diseases or parasites from your hotel sink when brushing your teeth or making tea in your room. In fact, some cities like Kyoto pride themselves on the quality of the water, citing its purity and sweet flavor. There are also an abundance of vending machines in Japan, especially at train and subway stations where you can buy bottled water or interesting named drinks like Pocari Sweat (which is pretty good!).
Do be careful if you are considering water from a source that is not specifically designated for human consumption. For example, avoid filling a drinking bottle at a spigot used for watering plants or in the small sink at the top of a toilet tank. Sometimes these use grey water from other sources to conserve water.
Centuries ago, pure water was not always the case, and so for everyday use people tended to drink barley tea, called mugi cha, because preparing the tea by boiling sterilized it. Even today, mugi cha is popular in the summer months, and many restaurants serve it in place of drinking water with a meal. It has a light brown color and earthy taste, and is served cold. Other restaurants serve green tea or genmai cha, which is a blend of green tea and toasted rice. If you do not like the taste, most restaurants are happy to provide regular water upon request.